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Escherichia coli K-12 substr. MG1655 Protein: ribosome

Subunit composition of ribosome = [(RrsA)(RpsA)(RpsB)(RpsC)(RpsD)(RpsE)(RpsF)(RpsG)(RpsH)(RpsI)(RpsJ)(RpsK)(RpsL)(RpsM)(RpsN)(RpsO)(RpsP)(RpsQ)(RpsR)(RpsS)(RpsT)(RpsU)(Sra)][(RrlA)(RrfA)(RplA)(RplB)(RplC)(RplD)(RplE)(RplF)([RplJ][(RplL)2]2)(RplI)(RplK)(RplM)(RplN)(RplO)(RplP)(RplQ)(RplR)(RplS)(RplT)(RplU)(RplV)(RplW)(RplX)(RplY)(RpmA)(RpmB)(RpmC)(RpmD)(RpmE)(RpmF)(RpmG)(RpmH)(RpmI)(RpmJ)]
         30S ribosomal subunit = (RrsA)(RpsA)(RpsB)(RpsC)(RpsD)(RpsE)(RpsF)(RpsG)(RpsH)(RpsI)(RpsJ)(RpsK)(RpsL)(RpsM)(RpsN)(RpsO)(RpsP)(RpsQ)(RpsR)(RpsS)(RpsT)(RpsU)(Sra) (summary available)
                 16S ribosomal RNA (rrsA) = RrsA (extended summary available)
                 30S ribosomal subunit protein S1 = RpsA (extended summary available)
                 30S ribosomal subunit protein S2 = RpsB (summary available)
                 30S ribosomal subunit protein S3 = RpsC (summary available)
                 30S ribosomal subunit protein S4 = RpsD (extended summary available)
                 30S ribosomal subunit protein S5 = RpsE (extended summary available)
                 30S ribosomal subunit protein S6 = RpsF (extended summary available)
                 30S ribosomal subunit protein S7 = RpsG (extended summary available)
                 30S ribosomal subunit protein S8 = RpsH (extended summary available)
                 30S ribosomal subunit protein S9 = RpsI (extended summary available)
                 30S ribosomal subunit protein S10 = RpsJ (extended summary available)
                 30S ribosomal subunit protein S11 = RpsK (summary available)
                 30S ribosomal subunit protein S12 = RpsL (extended summary available)
                 30S ribosomal subunit protein S13 = RpsM (extended summary available)
                 30S ribosomal subunit protein S14 = RpsN (summary available)
                 30S ribosomal subunit protein S15 = RpsO (extended summary available)
                 30S ribosomal subunit protein S16 = RpsP (summary available)
                 30S ribosomal subunit protein S17 = RpsQ (summary available)
                 30S ribosomal subunit protein S18 = RpsR (extended summary available)
                 30S ribosomal subunit protein S19 = RpsS (summary available)
                 30S ribosomal subunit protein S20 = RpsT (extended summary available)
                 30S ribosomal subunit protein S21 = RpsU (summary available)
                 30S ribosomal subunit protein S22 = Sra (summary available)
         50S ribosomal subunit = (RrlA)(RrfA)(RplA)(RplB)(RplC)(RplD)(RplE)(RplF)([RplJ][(RplL)2]2)(RplI)(RplK)(RplM)(RplN)(RplO)(RplP)(RplQ)(RplR)(RplS)(RplT)(RplU)(RplV)(RplW)(RplX)(RplY)(RpmA)(RpmB)(RpmC)(RpmD)(RpmE)(RpmF)(RpmG)(RpmH)(RpmI)(RpmJ)
                 23S ribosomal RNA (rrlA) = RrlA (extended summary available)
                 5S ribosomal RNA (rrfA) = RrfA (extended summary available)
                 50S ribosomal subunit protein L1 = RplA (extended summary available)
                 50S ribosomal subunit protein L2 = RplB (summary available)
                 50S ribosomal subunit protein L3 = RplC (summary available)
                 50S ribosomal subunit protein L4 = RplD (extended summary available)
                 50S ribosomal subunit protein L5 = RplE (summary available)
                 50S ribosomal subunit protein L6 = RplF (summary available)
                 50S ribosomal protein complex L8 = (RplJ)([RplL]2)2 (summary available)
                         50S ribosomal subunit protein L10 = RplJ (extended summary available)
                         50S ribosomal subunit protein L7/L12 dimer = (RplL)2
                                 50S ribosomal subunit protein L12 = RplL
                 50S ribosomal subunit protein L9 = RplI (summary available)
                 50S ribosomal subunit protein L11 = RplK (extended summary available)
                 50S ribosomal subunit protein L13 = RplM (extended summary available)
                 50S ribosomal subunit protein L14 = RplN (extended summary available)
                 50S ribosomal subunit protein L15 = RplO (summary available)
                 50S ribosomal subunit protein L16 = RplP (extended summary available)
                 50S ribosomal subunit protein L17 = RplQ (summary available)
                 50S ribosomal subunit protein L18 = RplR (extended summary available)
                 50S ribosomal subunit protein L19 = RplS (extended summary available)
                 50S ribosomal subunit protein L20 = RplT (extended summary available)
                 50S ribosomal subunit protein L21 = RplU (summary available)
                 50S ribosomal subunit protein L22 = RplV (extended summary available)
                 50S ribosomal subunit protein L23 = RplW (extended summary available)
                 50S ribosomal subunit protein L24 = RplX (summary available)
                 50S ribosomal subunit protein L25 = RplY (summary available)
                 50S ribosomal subunit protein L27 = RpmA (extended summary available)
                 50S ribosomal subunit protein L28 = RpmB (summary available)
                 50S ribosomal subunit protein L29 = RpmC (summary available)
                 50S ribosomal subunit protein L30 = RpmD (summary available)
                 50S ribosomal subunit protein L31 = RpmE (summary available)
                 50S ribosomal subunit protein L32 = RpmF (summary available)
                 50S ribosomal subunit protein L33 = RpmG (summary available)
                 50S ribosomal subunit protein L34 = RpmH (summary available)
                 50S ribosomal subunit protein L35 = RpmI (summary available)
                 50S ribosomal subunit protein L36 = RpmJ (summary available)

Summary:
The ribosome is a complex machinery that translates the genetic code.

A crystal structure of the E. coli ribosome has been determined at 3.5 Å resolution [Schuwirth05]. Additional crystal structures of the ribosome with tRNA bound in two functionally distinct states reveal how a ratchet-like motion of the small and large subunits contributes to translocation, termination of translation, and ribosome recycling [Zhang09a, Dunkle11].

Approximately eight molecules of Zn2+ are bound to the ribosome; therefore, it appears that a large fraction of intracellular Zn2+ is ribosome-associated [Hensley11].

Selected reviews: [Ramakrishnan02, Yonath05, Ogle05, Kaczanowska07]

Citations: [Kuhlenkoetter11]

Relationship Links: PDB:Structure:3R8N , PDB:Structure:3R8O , PDB:Structure:3R8S , PDB:Structure:3R8T

Gene-Reaction Schematic: ?

Credits:
Created 15-Jun-2006 by Keseler I , SRI International


Subunit of ribosome: 30S ribosomal subunit

Synonyms: ribosome, small subunit

Relationship Links: PDB:Structure:1P6G , PDB:Structure:1P87 , PDB:Structure:2AVY

Summary:
Assembly of the 30S ribosomal subunit has been studied in real time. Initial assembly is linked to the formation of structured 16S rRNA regions, while later steps involve induced fit between ribosomal proteins and the rRNA [Adilakshmi08]. Discovery single-particle profiling was used to visualize assembly of the 30S ribosomal subunit by indentifying and following changes among 14 subunit assembly intermediates over time [Mulder10]. The kinetically favored assembly pathway of the 30S preinitiation complex has been determined [Milon12].

The function of the ribosomal P site has been reviewed [Noller05].


Subunit of 30S ribosomal subunit: 16S ribosomal RNA (rrsA)

Synonyms: rrsA

Gene: rrsA Accession Numbers: EG30084 (EcoCyc), b3851, ECK3843

Sequence Length: 513 AAs

MultiFun Terms: cell structure ribosomes
information transfer protein related translation
information transfer RNA related rRNA, stable RNA

Unification Links: EcoliWiki:b3851

Reactions known to consume the compound:

Not in pathways:
rRNA + S-adenosyl-L-methionine → rRNA containing N6,N6-dimethyladenine + S-adenosyl-L-homocysteine

Reactions known to produce the compound:

tRNA processing :
a tRNA precursor with a 5' extension and a short 3' extension + H2O → a tRNA precursor with a short 3' extension + a single-stranded RNA
a tRNA precursor with a 5' extension + H2O → an uncharged tRNA + a single-stranded RNA

Not in pathways:
an mRNA + H2O → a single-stranded RNA + a single-stranded RNA
an mRNA + H2O → a single-stranded RNA + a single-stranded RNA
RNase E degradation substrate mRNA + n H2O → n a single-stranded RNA
YhaV endonuclease degradation substrate rRNA + H2O → 2 a single-stranded RNA
YhaV endonuclease degradation substrate mRNA + H2O → 2 a single-stranded RNA
RNase III mRNA processing substrate + 2 H2O → RNase III processing product mRNA + 2 a single-stranded RNA
23S rRNA[periplasmic space] + H2O[periplasmic space] → 2 a single-stranded RNA[periplasmic space]
an mRNA[periplasmic space] + H2O[periplasmic space] → 2 a single-stranded RNA[periplasmic space]
RNase G degradation substrate mRNA + H2O → 2 a single-stranded RNA
9S rRNA + 2 H2O → 5S rRNA + 2 a single-stranded RNA
RNase E mRNA processing substrate + n H2O → RNase E processing product mRNA + n a single-stranded RNA

Reactions known to both consume and produce the compound:

Not in pathways:
a single-stranded RNA + phosphate ↔ a single-stranded RNA + a nucleoside diphosphate

In Reactions of unknown directionality:

Not in pathways:
rRNA[periplasmic space] = 2 a single-stranded RNA[periplasmic space]


rRNA[periplasmic space] = 2 a single-stranded RNA[periplasmic space]

Summary:
The 16S rRNA is the RNA component of the small subunit (30S subunit) of the E. coli ribosome.

There are seven ribosomal RNA (rRNA) operons, called rrsA, rrsB, rrsC, rrsD, rrsE, rrsG, and rrsH. Each operon contains a 16S rRNA gene, a 23S rRNA gene, and a 5S rRNA gene (except the rrsD operon, which contains two 5S rRNA genes) interspersed with various tRNA genes. Regarding nomenclature, "rrs" genes encode 16S rRNAs, "rrl" genes encode 23S rRNAs, and "rrf" genes encode 5S rRNAs [Neidhardt96].

16S rRNA has been studied extensively. Its sequence and structure has been described, its relationship to ribosome assembly, structure, and function has been characterized, interactions between the 16S rRNA and ribosomal proteins have been described, mutants have been analyzed. 16S rRNA is subject to post-transcriptional processing, methylation, and pseudouridylation. Possible roles for the modified nucleotides have been proposed [Sergiev07].

The 16S rRNA is targeted by a number of antibiotic agents. The functional interactions between antibiotic sensitivity and 16S rRNA have been examined in detail.

Reviews describing these results are available.

Regulation has been described in detail; for a review see [Schneider03].

Reviews: [Ganoza77, Garrett77, Brimacombe78, Azad79, Thompson83, Woese83, Moore88, Brimacombe88, Dahlberg89, Stern89, Leclerc90, Craigen90, Srivastava91, Brimacombe91, Scheinman92, Brimacombe92, Laughrea94, Tuite94, Triman95, Triman94, Easterwood95, Mueller95, BrakierGingras95, Groisman95, Ehresmann95, Triman96, Triman97, Moore97, Altman97, Nagano97, Triman98, Ashraf97, Lee01a, Recht01]


Subunit of 30S ribosomal subunit: 30S ribosomal subunit protein S1

Synonyms: SsyF, RpsA

Gene: rpsA Accession Numbers: EG10900 (EcoCyc), b0911, ECK0902

Locations: ribosome, membrane, cytosol

Sequence Length: 557 AAs

Molecular Weight: 61.158 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred from experiment Inferred by computational analysis [GOA01, Sorensen98]
GO:2000766 - negative regulation of cytoplasmic translation Inferred from experiment [Skouv90]
Molecular Function: GO:0003723 - RNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA01, Wower04]
GO:0003729 - mRNA binding Inferred from experiment [Koleva06]
GO:0003735 - structural constituent of ribosome Inferred from experiment Inferred by computational analysis [GOA01, Byrgazov12]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment [Lasserre06]
GO:0016020 - membrane Inferred from experiment [Lasserre06]
GO:0022627 - cytosolic small ribosomal subunit Inferred from experiment [Hindennach71, Subramanian77]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-35884N , EcoliWiki:b0911 , Mint:MINT-1315122 , ModBase:P0AG67 , PR:PRO_000023854 , Pride:P0AG67 , Protein Model Portal:P0AG67 , RefSeq:NP_415431 , SMR:P0AG67 , String:511145.b0911 , UniProt:P0AG67

Relationship Links: InterPro:IN-FAMILY:IPR000110 , InterPro:IN-FAMILY:IPR003029 , InterPro:IN-FAMILY:IPR012340 , InterPro:IN-FAMILY:IPR022967 , PDB:Structure:2BH8 , PDB:Structure:2KHI , PDB:Structure:2KHJ , Pfam:IN-FAMILY:PF00575 , Prints:IN-FAMILY:PR00681 , Prosite:IN-FAMILY:PS50126 , Smart:IN-FAMILY:SM00316

Summary:
The S1 protein is essential in E. coli; it is a component of the ribosome and is likely required for translation of most mRNAs [Sorensen98]. During translation initiation, mRNAs are selected and bound to the ribosome with the help of two components: the conserved 3' end of 16S rRNA is complementary to the Shine-Dalgarno region of the typical mRNA, while the S1 protein binds to the leader sequence of mRNAs, upstream of the Shine-Dalgarno region [Boni91, Komarova02]. S1 promotes RNA strand displacement in vitro [Rajkowitsch07]. The S1 protein is not required for the translation of leaderless mRNAs [Tedin97, Moll02, Byrgazov12]. Association of S1 with the ribosome is unstable [Subramanian77], and the S2 protein is required for binding of S1 to the 30S subunit of the ribosome [Moll02]. The N-terminal domain of S1 is necessary and sufficient for interaction with S2 and for ribosome binding [Byrgazov12].

The S1 protein is the largest of the ribosomal proteins and assumes a complex elongated shape; it is located at the junction of the head, platform, and main body of the 30S subunit [Sengupta01]. RNA binding is associated with structural modification of the S1 protein [Aliprandi08]. NMR structures of domains 4 and 6 have been determined [Salah09].

The translation initiation region of rpsA mRNA, which encodes the S1 protein, lacks a canonical Shine-Dalgarno region, but nevertheless supports high levels of translation [Skorski06]. Expression of S1 is autoregulated; the S1 protein acts as a specific repressor of translation of its own mRNA [Christiansen81, Skouv90]. The N-terminus of S1 is sufficient for repressing rpsA expression [Skouv90]. Supported by various types of evidence including site-directed mutagenesis, footprinting and phylogenetic studies, a model was proposed in which the rpsA leader region folds into three stem-loop structures which enable efficient translation; binding of free S1 protein disturbs the conformation of the rpsA mRNA and thus specifically represses translation [Boni01, Tchufistova03].

S1 proteins carrying a C-terminal truncation due to IS10R insertion in the ssyF29 mutant lack the R4 RNA binding domain and display a growth defect [Boni00]. The growth defect was found to be due to destabilization of the rpsA mRNA [Skorski07].

The S1 protein has been suggested to play a role in trans-translation by binding transfer-messenger RNA (tmRNA) and delivering it to stalled ribosomes [Bordeau02, Karzai01, Wower00, Wower04, Okada04]. An alternative model suggests that S1 binds to both mRNA and tmRNA molecules indiscriminately and may not play a direct role in tmRNA-mediated tagging of incompletely translated polypeptides [McGinness04]. Later studies disagree on whether S1 is [Saguy07] or is not [Qi07] required for trans-translation in vitro.

The S1 protein has been reported to bind to RNA polymerase and stimulate transcription of a number of promoters [Sukhodolets03]. S1 activates transcriptional cycling in vitro [Sukhodolets06]. S1 may also inhibit RNase E-dependent mRNA decay [Delvillani11].

ssyF: "suppressor of secY24(Ts)" [Shiba86]

Citations: [Pan11]

Essentiality data for rpsA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 30S ribosomal subunit: 30S ribosomal subunit protein S2

Synonyms: RpsB

Gene: rpsB Accession Numbers: EG10901 (EcoCyc), b0169, ECK0168

Locations: ribosome

Sequence Length: 241 AAs

Molecular Weight: 26.744 kD (from nucleotide sequence)

Molecular Weight: 29.2 kD (experimental) [Georgalis81]

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Cooperman81, Butland05]
GO:0008270 - zinc ion binding Inferred from experiment [Katayama02]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
Cellular Component: GO:0022627 - cytosolic small ribosomal subunit Inferred from experiment [Hindennach71, WittmannLiebold73, WittmannLiebold81]
GO:0005622 - intracellular Inferred by computational analysis [GOA01]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0015935 - small ribosomal subunit Inferred by computational analysis [GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: EcoliWiki:b0169 , PR:PRO_000023855 , Pride:P0A7V0 , Protein Model Portal:P0A7V0 , RefSeq:NP_414711 , SMR:P0A7V0 , String:511145.b0169 , UniProt:P0A7V0

Relationship Links: InterPro:IN-FAMILY:IPR001865 , InterPro:IN-FAMILY:IPR005706 , InterPro:IN-FAMILY:IPR018130 , InterPro:IN-FAMILY:IPR023591 , Panther:IN-FAMILY:PTHR12534 , PDB:Structure:1M5G , PDB:Structure:1P87 , PDB:Structure:1VS5 , PDB:Structure:1VS7 , PDB:Structure:2AVY , PDB:Structure:2AW7 , PDB:Structure:2GY9 , PDB:Structure:2GYB , PDB:Structure:2I2P , PDB:Structure:2I2U , PDB:Structure:2QAL , PDB:Structure:2QAN , PDB:Structure:2QB9 , PDB:Structure:2QBB , PDB:Structure:2QBD , PDB:Structure:2QBF , PDB:Structure:2QBH , PDB:Structure:2QBJ , PDB:Structure:2QOU , PDB:Structure:2QOW , PDB:Structure:2QOY , PDB:Structure:2QP0 , PDB:Structure:2VHO , PDB:Structure:2VHP , PDB:Structure:2WWL , PDB:Structure:2YKR , PDB:Structure:2Z4K , PDB:Structure:2Z4M , PDB:Structure:3DF1 , PDB:Structure:3DF3 , PDB:Structure:3E1A , PDB:Structure:3E1C , PDB:Structure:3FIH , PDB:Structure:3I1M , PDB:Structure:3I1O , PDB:Structure:3I1Q , PDB:Structure:3I1S , PDB:Structure:3I1Z , PDB:Structure:3I21 , PDB:Structure:3IZV , PDB:Structure:3IZW , PDB:Structure:3J00 , PDB:Structure:3J0U , PDB:Structure:3J0V , PDB:Structure:3J0X , PDB:Structure:3J0Z , PDB:Structure:3J10 , PDB:Structure:3J13 , PDB:Structure:3J18 , PDB:Structure:3J36 , PDB:Structure:3KC4 , PDB:Structure:3OAQ , PDB:Structure:3OAR , PDB:Structure:3OFA , PDB:Structure:3OFB , PDB:Structure:3OFO , PDB:Structure:3OFP , PDB:Structure:3OFX , PDB:Structure:3OFY , PDB:Structure:3OR9 , PDB:Structure:3ORA , PDB:Structure:3SFS , PDB:Structure:3UOQ , PDB:Structure:4A2I , PDB:Structure:4ADV , PDB:Structure:4GAQ , PDB:Structure:4GAS , PDB:Structure:4GD1 , PDB:Structure:4GD2 , PDB:Structure:4KIY , PDB:Structure:4KJ0 , PDB:Structure:4KJ2 , PDB:Structure:4KJ4 , PDB:Structure:4KJ6 , PDB:Structure:4KJ8 , PDB:Structure:4KJA , PDB:Structure:4KJC , Pfam:IN-FAMILY:PF00318 , Prints:IN-FAMILY:PR00395 , Prosite:IN-FAMILY:PS00962 , Prosite:IN-FAMILY:PS00963

Summary:
The S2 protein, a component of the 30S subunit of the ribosome, is essential in E. coli [Bollen79]. S2 is required for S1 binding to the ribosome [Moll02]. Overexpression of csdA, a DEAD-box RNA helicase, supresses the defect of a temperature-sensitive allele of rpsB [Toone91] by restoring assembly of both S1 and S2 with the ribosome at the non-permissive temperature [Moll02].

Expression of S2 is autoregulated, involving conserved elements located in the 5' UTR of the rpsB-tsf mRNA. Regulation may also involve the S1 protein [Aseev08].

Purified S2 protein binds to inorganic polyphosphate (polyP). In the presence of polyP, S2 forms a complex with the Lon protease and is degraded by it [Kuroda01, Nishii05]. S2 was also shown to crosslink to IF3 [Cooperman81].

A low-resolution cryo-electron microscopy map of the ribosome containing S2 has been analyzed [Gao03a].

Essentiality data for rpsB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 30S ribosomal subunit: 30S ribosomal subunit protein S3

Synonyms: RpsC

Gene: rpsC Accession Numbers: EG10902 (EcoCyc), b3314, ECK3301

Locations: cytosol, ribosome

Sequence Length: 233 AAs

Molecular Weight: 25.983 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0000737 - DNA catabolic process, endonucleolytic Inferred by computational analysis [Gaudet10]
GO:0002181 - cytoplasmic translation Inferred by computational analysis [Gaudet10]
GO:0006281 - DNA repair Inferred by computational analysis [Gaudet10]
GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
GO:0042981 - regulation of apoptotic process Inferred by computational analysis [Gaudet10]
Molecular Function: GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0003729 - mRNA binding Inferred by computational analysis [GOA06]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01, Gaudet10]
GO:0003906 - DNA-(apurinic or apyrimidinic site) lyase activity Inferred by computational analysis [Gaudet10]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022627 - cytosolic small ribosomal subunit Inferred from experiment [Hindennach71, WittmannLiebold73]
GO:0005622 - intracellular Inferred by computational analysis [GOA01]
GO:0005634 - nucleus Inferred by computational analysis [Gaudet10]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0015935 - small ribosomal subunit Inferred by computational analysis [GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-35807N , EcoliWiki:b3314 , Mint:MINT-6478122 , PR:PRO_000023856 , Pride:P0A7V3 , Protein Model Portal:P0A7V3 , RefSeq:NP_417773 , SMR:P0A7V3 , String:511145.b3314 , UniProt:P0A7V3

Relationship Links: InterPro:IN-FAMILY:IPR001351 , InterPro:IN-FAMILY:IPR004044 , InterPro:IN-FAMILY:IPR004087 , InterPro:IN-FAMILY:IPR005704 , InterPro:IN-FAMILY:IPR009019 , InterPro:IN-FAMILY:IPR015946 , InterPro:IN-FAMILY:IPR018280 , PDB:Structure:1M5G , PDB:Structure:1P6G , PDB:Structure:1P87 , PDB:Structure:1VS5 , PDB:Structure:1VS7 , PDB:Structure:2AVY , PDB:Structure:2AW7 , PDB:Structure:2GY9 , PDB:Structure:2GYB , PDB:Structure:2I2P , PDB:Structure:2I2U , PDB:Structure:2QAL , PDB:Structure:2QAN , PDB:Structure:2QB9 , PDB:Structure:2QBB , PDB:Structure:2QBD , PDB:Structure:2QBF , PDB:Structure:2QBH , PDB:Structure:2QBJ , PDB:Structure:2QOU , PDB:Structure:2QOW , PDB:Structure:2QOY , PDB:Structure:2QP0 , PDB:Structure:2VHO , PDB:Structure:2VHP , PDB:Structure:2WWL , PDB:Structure:2YKR , PDB:Structure:2Z4K , PDB:Structure:2Z4M , PDB:Structure:3DF1 , PDB:Structure:3DF3 , PDB:Structure:3E1A , PDB:Structure:3E1C , PDB:Structure:3FIH , PDB:Structure:3I1M , PDB:Structure:3I1O , PDB:Structure:3I1Q , PDB:Structure:3I1S , PDB:Structure:3I1Z , PDB:Structure:3I21 , PDB:Structure:3IZV , PDB:Structure:3IZW , PDB:Structure:3J00 , PDB:Structure:3J0U , PDB:Structure:3J0V , PDB:Structure:3J0X , PDB:Structure:3J0Z , PDB:Structure:3J10 , PDB:Structure:3J13 , PDB:Structure:3J18 , PDB:Structure:3J36 , PDB:Structure:3KC4 , PDB:Structure:3OAQ , PDB:Structure:3OAR , PDB:Structure:3OFA , PDB:Structure:3OFB , PDB:Structure:3OFO , PDB:Structure:3OFP , PDB:Structure:3OFX , PDB:Structure:3OFY , PDB:Structure:3OR9 , PDB:Structure:3ORA , PDB:Structure:3SFS , PDB:Structure:3UOQ , PDB:Structure:4A2I , PDB:Structure:4ADV , PDB:Structure:4GAQ , PDB:Structure:4GAS , PDB:Structure:4GD1 , PDB:Structure:4GD2 , PDB:Structure:4KIY , PDB:Structure:4KJ0 , PDB:Structure:4KJ2 , PDB:Structure:4KJ4 , PDB:Structure:4KJ6 , PDB:Structure:4KJ8 , PDB:Structure:4KJA , PDB:Structure:4KJC , Pfam:IN-FAMILY:PF00189 , Pfam:IN-FAMILY:PF07650 , Prosite:IN-FAMILY:PS00548 , Prosite:IN-FAMILY:PS50823 , Smart:IN-FAMILY:SM00322

Summary:
The S3 protein, a component of the small subunit of the ribosome, is surface-accessible and located on the head of the 30S subunit [Breitenreuter84]. It can be crosslinked to rRNA [Urlaub95] and nascent peptides [Choi98] as well as to IF3 [Cooperman81]. S3 is the main target of modification by reaction with pyridoxal phosphate [Ohsawa83].

The ribosome was found to have mRNA helicase activity, and mutations in the S3 and S4 subunits impair this activity [Takyar05].

A low-resolution cryo-electron microscopy map of the ribosome containing S3 has been analyzed [Gao03a].

Essentiality data for rpsC knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 30S ribosomal subunit: 30S ribosomal subunit protein S4

Synonyms: RamA, RpsD

Gene: rpsD Accession Numbers: EG10903 (EcoCyc), b3296, ECK3283

Locations: cytosol, ribosome

Sequence Length: 206 AAs

Molecular Weight: 23.469 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0031564 - transcription antitermination Inferred from experiment [Torres01]
GO:0045947 - negative regulation of translational initiation Inferred from experiment [Yates80]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0006353 - DNA-templated transcription, termination Inferred by computational analysis [UniProtGOA11]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
GO:0006417 - regulation of translation Inferred by computational analysis [UniProtGOA11]
GO:0046677 - response to antibiotic Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0000900 - translation repressor activity, nucleic acid binding Inferred from experiment [Tang90]
GO:0005515 - protein binding Inferred from experiment [Torres01]
GO:0019843 - rRNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA06, GOA01, Mizushima70]
GO:0048027 - mRNA 5'-UTR binding Inferred from experiment [Deckman87]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022627 - cytosolic small ribosomal subunit Inferred from experiment [Hindennach71]
GO:0005622 - intracellular Inferred by computational analysis [GOA01]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11]
GO:0015935 - small ribosomal subunit Inferred by computational analysis [GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-35794N , EcoliWiki:b3296 , Mint:MINT-6478162 , PR:PRO_000023857 , Pride:P0A7V8 , Protein Model Portal:P0A7V8 , RefSeq:NP_417755 , SMR:P0A7V8 , String:511145.b3296 , UniProt:P0A7V8

Relationship Links: InterPro:IN-FAMILY:IPR001912 , InterPro:IN-FAMILY:IPR002942 , InterPro:IN-FAMILY:IPR005709 , InterPro:IN-FAMILY:IPR018079 , InterPro:IN-FAMILY:IPR022801 , Panther:IN-FAMILY:PTHR11831 , PDB:Structure:1EG0 , PDB:Structure:1M5G , PDB:Structure:1P6G , PDB:Structure:1P87 , PDB:Structure:1VS5 , PDB:Structure:1VS7 , PDB:Structure:2AVY , PDB:Structure:2AW7 , PDB:Structure:2GY9 , PDB:Structure:2GYB , PDB:Structure:2I2P , PDB:Structure:2I2U , PDB:Structure:2QAL , PDB:Structure:2QAN , PDB:Structure:2QB9 , PDB:Structure:2QBB , PDB:Structure:2QBD , PDB:Structure:2QBF , PDB:Structure:2QBH , PDB:Structure:2QBJ , PDB:Structure:2QOU , PDB:Structure:2QOW , PDB:Structure:2QOY , PDB:Structure:2QP0 , PDB:Structure:2VHP , PDB:Structure:2WWL , PDB:Structure:2YKR , PDB:Structure:2Z4K , PDB:Structure:2Z4M , PDB:Structure:3DF1 , PDB:Structure:3DF3 , PDB:Structure:3E1A , PDB:Structure:3E1C , PDB:Structure:3FIH , PDB:Structure:3I1M , PDB:Structure:3I1O , PDB:Structure:3I1Q , PDB:Structure:3I1S , PDB:Structure:3I1Z , PDB:Structure:3I21 , PDB:Structure:3IZV , PDB:Structure:3IZW , PDB:Structure:3J00 , PDB:Structure:3J0U , PDB:Structure:3J0V , PDB:Structure:3J0X , PDB:Structure:3J0Z , PDB:Structure:3J10 , PDB:Structure:3J13 , PDB:Structure:3J18 , PDB:Structure:3J36 , PDB:Structure:3KC4 , PDB:Structure:3OAQ , PDB:Structure:3OAR , PDB:Structure:3OFA , PDB:Structure:3OFB , PDB:Structure:3OFO , PDB:Structure:3OFP , PDB:Structure:3OFX , PDB:Structure:3OFY , PDB:Structure:3OR9 , PDB:Structure:3ORA , PDB:Structure:3SFS , PDB:Structure:3UOQ , PDB:Structure:4A2I , PDB:Structure:4ADV , PDB:Structure:4GAQ , PDB:Structure:4GAS , PDB:Structure:4GD1 , PDB:Structure:4GD2 , PDB:Structure:4KIY , PDB:Structure:4KJ0 , PDB:Structure:4KJ2 , PDB:Structure:4KJ4 , PDB:Structure:4KJ6 , PDB:Structure:4KJ8 , PDB:Structure:4KJA , PDB:Structure:4KJC , Pfam:IN-FAMILY:PF00163 , Pfam:IN-FAMILY:PF01479 , Prosite:IN-FAMILY:PS00632 , Prosite:IN-FAMILY:PS50889 , Smart:IN-FAMILY:SM00363

Summary:
The S4 protein, a component of the 30S subunit of the ribosome, functions in the assembly of the 30S ribosomal subunit, the mRNA helicase activity of the ribosome, the regulation of translation of a subset of ribosomal proteins, and transcription antitermination of rRNA operons.

S4 interacts directly with helical elements at the 5' domain of the 16S rRNA [Stern86, Powers95, Vartikar89, Bellur09, Ramaswamy09]. The N-terminal domain of unbound S4 is dynamically disordered, which is exploited to initiate S4 binding to helix 16 in the unfolded five-way junction of 16S rRNA [Chen10]. S4 binding stabilizes the five-way junction and the helix 18 pseudoknot; both become tightly folded within the first minute of S4 binding. Other components of the five-way junction require more time and perhaps other 30S proteins to achieve their final conformation [Mayerle11]. The ability of both S4 and S7 to bind 16S rRNA by themselves indicates that they function as initiator proteins for the assembly of the 30S subunit of the ribosome. The S20, S16, S15, S6, and S8 subunits appear to depend on S4 for assembly [Nowotny88].

The S4 protein is involved in the regulation of translation of the other ribosomal proteins encoded by the α operon, RpsM (S13), RpsK (S11), RplQ (L17) and S4 itself [Yates80, Thomas87, JinksRobertson82]. The α operon leader region is required for translational repression by S4 [Thomas87]; S4 specifically interacts with a double pseudoknot structure which overlaps with the ribosome binding site and initiation codon for RpsM [Deckman85, Deckman87, Deckman87a, Tang89, Tang90, Gluick95]. There may be a second binding site for S4 upstream of the RplQ open reading frame [Meek84]. The same protein domain appears to be responsible for both mRNA and rRNA binding [Baker95, Conrad87].

S4 can also act as a general transcription antitermination factor similar to NusA; it associates with RNA polymerase and is involved in rRNA operon antitermination [Torres01].

S4 influences translational fidelity [Topisirovic77]. Certain mutations in rpsD confer a "ribosomal ambiguity" (ram) phenotype, which is characterized by decreased growth rate, increased streptomycin sensitivity, and increased errors in translation [Zimmermann71, Andersson83, Andersson82, Olsson79]. Ribosomes containing the S4 rpsD12 allele display the ram phenotype; these ribosomes appear to exploit only the initial phase of tRNA selection, thus reducing discrimination against near-cognate aa-tRNAs [Zaher10]. Cells carrying the rpsD14 allele have a mutator phenotype [Balashov03]. The ribosome was found to have mRNA helicase activity, and mutations in the S3 and S4 subunits impair this activity [Takyar05].

ramA: "ribosomal ambiguity"

Citations: [Bedwell85]

Essentiality data for rpsD knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 30S ribosomal subunit: 30S ribosomal subunit protein S5

Synonyms: Spc, Eps, SpcA, RpsE

Gene: rpsE Accession Numbers: EG10904 (EcoCyc), b3303, ECK3290

Locations: cytosol, ribosome

Sequence Length: 167 AAs

Molecular Weight: 17.603 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
GO:0046677 - response to antibiotic Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Arifuzzaman06, Butland05]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA06, GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022627 - cytosolic small ribosomal subunit Inferred from experiment [Hindennach71]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0015935 - small ribosomal subunit Inferred by computational analysis [GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11, GOA06]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: EcoliWiki:b3303 , Mint:MINT-6478202 , ModBase:P0A7W1 , PR:PRO_000023858 , Pride:P0A7W1 , Protein Model Portal:P0A7W1 , RefSeq:NP_417762 , SMR:P0A7W1 , String:511145.b3303 , UniProt:P0A7W1

Relationship Links: InterPro:IN-FAMILY:IPR000851 , InterPro:IN-FAMILY:IPR005324 , InterPro:IN-FAMILY:IPR005712 , InterPro:IN-FAMILY:IPR013810 , InterPro:IN-FAMILY:IPR014720 , InterPro:IN-FAMILY:IPR014721 , InterPro:IN-FAMILY:IPR018192 , InterPro:IN-FAMILY:IPR020568 , Panther:IN-FAMILY:PTHR13718 , PDB:Structure:1EG0 , PDB:Structure:1M5G , PDB:Structure:1P6G , PDB:Structure:1P87 , PDB:Structure:1VS5 , PDB:Structure:1VS7 , PDB:Structure:2AVY , PDB:Structure:2AW7 , PDB:Structure:2GY9 , PDB:Structure:2GYB , PDB:Structure:2I2P , PDB:Structure:2I2U , PDB:Structure:2QAL , PDB:Structure:2QAN , PDB:Structure:2QB9 , PDB:Structure:2QBB , PDB:Structure:2QBD , PDB:Structure:2QBF , PDB:Structure:2QBH , PDB:Structure:2QBJ , PDB:Structure:2QOU , PDB:Structure:2QOW , PDB:Structure:2QOY , PDB:Structure:2QP0 , PDB:Structure:2VHO , PDB:Structure:2VHP , PDB:Structure:2WWL , PDB:Structure:2YKR , PDB:Structure:2Z4K , PDB:Structure:2Z4M , PDB:Structure:3DF1 , PDB:Structure:3DF3 , PDB:Structure:3E1A , PDB:Structure:3E1C , PDB:Structure:3FIH , PDB:Structure:3I1M , PDB:Structure:3I1O , PDB:Structure:3I1Q , PDB:Structure:3I1S , PDB:Structure:3I1Z , PDB:Structure:3I21 , PDB:Structure:3IZV , PDB:Structure:3IZW , PDB:Structure:3J00 , PDB:Structure:3J0U , PDB:Structure:3J0V , PDB:Structure:3J0X , PDB:Structure:3J0Z , PDB:Structure:3J10 , PDB:Structure:3J13 , PDB:Structure:3J18 , PDB:Structure:3J36 , PDB:Structure:3KC4 , PDB:Structure:3OAQ , PDB:Structure:3OAR , PDB:Structure:3OFA , PDB:Structure:3OFB , PDB:Structure:3OFO , PDB:Structure:3OFP , PDB:Structure:3OFX , PDB:Structure:3OFY , PDB:Structure:3OR9 , PDB:Structure:3ORA , PDB:Structure:3SFS , PDB:Structure:3UOQ , PDB:Structure:4A2I , PDB:Structure:4ADV , PDB:Structure:4GAQ , PDB:Structure:4GAS , PDB:Structure:4GD1 , PDB:Structure:4GD2 , PDB:Structure:4KIY , PDB:Structure:4KJ0 , PDB:Structure:4KJ2 , PDB:Structure:4KJ4 , PDB:Structure:4KJ6 , PDB:Structure:4KJ8 , PDB:Structure:4KJA , PDB:Structure:4KJC , Pfam:IN-FAMILY:PF00333 , Pfam:IN-FAMILY:PF03719 , Prosite:IN-FAMILY:PS00585 , Prosite:IN-FAMILY:PS50881

Summary:
The S5 protein is a component of the 30S subunit of the ribosome. It was suggested that S5 is positioned to have access to the interface between the 30S and 50S subunits of the ribosome [Culver99].

The N-terminal half of S5 contains the sites of mutations that confer resistance to spectinomycin [Piepersberg75, Dekio69, DeWilde73] and binds non-specifically to helix 34 of the 16S rRNA [Heilek96, Stern88]. S5 may be involved in modulating the conformation of the 16S rRNA [Lodmell97]. S5 can be cross-linked to mRNA [RinkeAppel91] and tRNA [Graifer89].

S5 influences translational fidelity. Certain mutations in rpsE confer a "ribosomal ambiguity" phenotype, which is characterized by decreased growth rate, increased streptomycin sensitivity, and increased errors in translation [Ito73, Hasenbank73].

The S5 protein is acetylated at the N-terminus [WittmannLiebold78, Arnold99]; mutants in the alanine acetyltransferase enzyme, RimJ, are temperature sensitive [Cumberlidge79, Yoshikawa87]. N-terminal acetylation of S5 and S18 correlates with correct folding of the platform and central pseudoknot domains of 16S rRNA [Clatterbuck13].

spcA: "spectinomycin"

Essentiality data for rpsE knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 30S ribosomal subunit: 30S ribosomal subunit protein S6

Synonyms: SdgH, RpsF

Gene: rpsF Accession Numbers: EG10905 (EcoCyc), b4200, ECK4196

Locations: cytosol, ribosome

Sequence Length: 131 AAs

Molecular Weight: 15.187 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Zheng11, Hauser14, Rajagopala14]
GO:0048027 - mRNA 5'-UTR binding Inferred from experiment [Matelska13]
GO:0070181 - small ribosomal subunit rRNA binding Inferred from experiment [Gregory84]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0022627 - cytosolic small ribosomal subunit Inferred from experiment [Hindennach71, WittmannLiebold73]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-10782N , EcoliWiki:b4200 , Mint:MINT-1279331 , ModBase:P02358 , PR:PRO_000023859 , Pride:P02358 , Protein Model Portal:P02358 , RefSeq:NP_418621 , SMR:P02358 , String:511145.b4200 , UniProt:P02358

Relationship Links: InterPro:IN-FAMILY:IPR000529 , InterPro:IN-FAMILY:IPR014717 , InterPro:IN-FAMILY:IPR020814 , InterPro:IN-FAMILY:IPR020815 , PDB:Structure:1EG0 , PDB:Structure:1M5G , PDB:Structure:1P6G , PDB:Structure:1P87 , PDB:Structure:1VS5 , PDB:Structure:1VS7 , PDB:Structure:2AVY , PDB:Structure:2AW7 , PDB:Structure:2GY9 , PDB:Structure:2GYB , PDB:Structure:2I2P , PDB:Structure:2I2U , PDB:Structure:2QAL , PDB:Structure:2QAN , PDB:Structure:2QB9 , PDB:Structure:2QBB , PDB:Structure:2QBD , PDB:Structure:2QBF , PDB:Structure:2QBH , PDB:Structure:2QBJ , PDB:Structure:2QOU , PDB:Structure:2QOW , PDB:Structure:2QOY , PDB:Structure:2QP0 , PDB:Structure:2VHO , PDB:Structure:2VHP , PDB:Structure:2WWL , PDB:Structure:2YKR , PDB:Structure:2Z4K , PDB:Structure:2Z4M , PDB:Structure:3DF1 , PDB:Structure:3DF3 , PDB:Structure:3E1A , PDB:Structure:3E1C , PDB:Structure:3FIH , PDB:Structure:3I1M , PDB:Structure:3I1O , PDB:Structure:3I1Q , PDB:Structure:3I1S , PDB:Structure:3I1Z , PDB:Structure:3I21 , PDB:Structure:3IY8 , PDB:Structure:3IZV , PDB:Structure:3IZW , PDB:Structure:3J00 , PDB:Structure:3J0U , PDB:Structure:3J0V , PDB:Structure:3J0X , PDB:Structure:3J0Z , PDB:Structure:3J10 , PDB:Structure:3J13 , PDB:Structure:3J18 , PDB:Structure:3J36 , PDB:Structure:3KC4 , PDB:Structure:3OAQ , PDB:Structure:3OAR , PDB:Structure:3OFA , PDB:Structure:3OFB , PDB:Structure:3OFO , PDB:Structure:3OFP , PDB:Structure:3OFX , PDB:Structure:3OFY , PDB:Structure:3OR9 , PDB:Structure:3ORA , PDB:Structure:3SFS , PDB:Structure:3UOQ , PDB:Structure:4A2I , PDB:Structure:4ADV , PDB:Structure:4GAQ , PDB:Structure:4GAS , PDB:Structure:4GD1 , PDB:Structure:4GD2 , PDB:Structure:4KIY , PDB:Structure:4KJ0 , PDB:Structure:4KJ2 , PDB:Structure:4KJ4 , PDB:Structure:4KJ6 , PDB:Structure:4KJ8 , PDB:Structure:4KJA , PDB:Structure:4KJC , Pfam:IN-FAMILY:PF01250 , Prosite:IN-FAMILY:PS01048

Summary:
The S6 protein is a component of the 30S subunit of the ribosome. S6 interacts with the central domain of 16S rRNA [Gregory84, Stern88].

The S6 protein contains glutamate residues at the C-terminus, only two of which are encoded by the rpsF gene [Reeh79, Schnier86]; up to four additional glutamate residues are added post-translationally by the RimK enzyme [Kang89]. This form of S6 accumulates when the soxR regulon is activated [Greenberg90]. In bacteriophage T7-infected cells, S6 is phosphorylated [Robertson94].

Expression analysis of rpsFp indicates that it may be autoregulated by one or more of its operon components [Nakayashiki13]. Coexpressed S6:S18 were found to bind to the rpsF 5'-UTR in a region with structural similarity to their binding site in 16S rRNA. S6 together with S18 may thus be responsible for autoregulation of the rpsF-priB-rpsR-rplI operon [Matelska13].

A class of mutations in rpsF supresses the temperature-sensitive growth defect of certain dnaG alleles [Britton97]. The rpsF292 allele, which introduces a stop codon in place of Glu98, is an effective suppressor of ΔrecG. The effect is due to both elimination of RpsF and lower expression of PriB [Mahdi12]. Both rimK and rpsF deletion mutants reduce the basal level of SOS response and increase resistance to hydroxyurea [Nakayashiki13].

SdgH: "supressor of dnaG" [Britton97]

Review: [Nesterchuk11]

Citations: [Mulder10, Tang14]

Essentiality data for rpsF knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Indeterminate 37 Aerobic 7   Yes [Baba06, Comment 3]
Low [Bubunenko07]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 4]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 3]

Subunit of 30S ribosomal subunit: 30S ribosomal subunit protein S7

Synonyms: RpsG

Gene: rpsG Accession Numbers: EG10906 (EcoCyc), b3341, ECK3328

Locations: cytosol, ribosome, membrane

Sequence Length: 179 AAs

Molecular Weight: 20.019 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0000028 - ribosomal small subunit assembly Inferred from experiment [Nowotny88]
GO:0017148 - negative regulation of translation Inferred from experiment [Dean81]
GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0003729 - mRNA binding Inferred from experiment [Saito94, Golovin06]
GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Lasserre06, Butland05, MartinezHackert09]
GO:0019843 - rRNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA06, Wower83]
GO:0000049 - tRNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0016020 - membrane Inferred from experiment [Lasserre06]
GO:0022627 - cytosolic small ribosomal subunit Inferred from experiment [Hindennach71, Lasserre06]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11]
GO:0015935 - small ribosomal subunit Inferred by computational analysis [GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-10783N , EcoliWiki:b3341 , Mint:MINT-1236482 , ModBase:P02359 , PR:PRO_000023860 , Pride:P02359 , Protein Model Portal:P02359 , RefSeq:NP_417800 , SMR:P02359 , String:511145.b3341 , UniProt:P02359

Relationship Links: InterPro:IN-FAMILY:IPR000235 , InterPro:IN-FAMILY:IPR005717 , InterPro:IN-FAMILY:IPR020606 , InterPro:IN-FAMILY:IPR023798 , Panther:IN-FAMILY:PTHR11205 , Panther:IN-FAMILY:PTHR11205:SF13 , PDB:Structure:1EG0 , PDB:Structure:1M5G , PDB:Structure:1ML5 , PDB:Structure:1P6G , PDB:Structure:1P87 , PDB:Structure:1VS5 , PDB:Structure:1VS7 , PDB:Structure:2AVY , PDB:Structure:2AW7 , PDB:Structure:2GY9 , PDB:Structure:2GYB , PDB:Structure:2I2P , PDB:Structure:2I2U , PDB:Structure:2QAL , PDB:Structure:2QAN , PDB:Structure:2QB9 , PDB:Structure:2QBB , PDB:Structure:2QBD , PDB:Structure:2QBF , PDB:Structure:2QBH , PDB:Structure:2QBJ , PDB:Structure:2QOU , PDB:Structure:2QOW , PDB:Structure:2QOY , PDB:Structure:2QP0 , PDB:Structure:2VHO , PDB:Structure:2VHP , PDB:Structure:2WWL , PDB:Structure:2YKR , PDB:Structure:2Z4K , PDB:Structure:2Z4M , PDB:Structure:3DF1 , PDB:Structure:3DF3 , PDB:Structure:3E1A , PDB:Structure:3E1C , PDB:Structure:3FIH , PDB:Structure:3I1M , PDB:Structure:3I1O , PDB:Structure:3I1Q , PDB:Structure:3I1S , PDB:Structure:3I1Z , PDB:Structure:3I21 , PDB:Structure:3IZV , PDB:Structure:3IZW , PDB:Structure:3J00 , PDB:Structure:3J0U , PDB:Structure:3J0V , PDB:Structure:3J0X , PDB:Structure:3J0Z , PDB:Structure:3J10 , PDB:Structure:3J13 , PDB:Structure:3J18 , PDB:Structure:3J36 , PDB:Structure:3KC4 , PDB:Structure:3OAQ , PDB:Structure:3OAR , PDB:Structure:3OFA , PDB:Structure:3OFB , PDB:Structure:3OFO , PDB:Structure:3OFP , PDB:Structure:3OFX , PDB:Structure:3OFY , PDB:Structure:3OR9 , PDB:Structure:3ORA , PDB:Structure:3SFS , PDB:Structure:3UOQ , PDB:Structure:4A2I , PDB:Structure:4ADV , PDB:Structure:4GAQ , PDB:Structure:4GAS , PDB:Structure:4GD1 , PDB:Structure:4GD2 , PDB:Structure:4KIY , PDB:Structure:4KJ0 , PDB:Structure:4KJ2 , PDB:Structure:4KJ4 , PDB:Structure:4KJ6 , PDB:Structure:4KJ8 , PDB:Structure:4KJA , PDB:Structure:4KJC , Pfam:IN-FAMILY:PF00177 , Prosite:IN-FAMILY:PS00052

Summary:
The S7 protein is a component of the 30S subunit of the ribosome.

S7 binds to 16S rRNA [Ehresmann76, Wower83, Hajnsdorf86, Chiaruttini86, Wiener87, Wiener88, Urlaub95, Dragon93, Dragon94, Robert00]. The ability of both S4 and S7 to bind 16S rRNA by themselves indicates that they function as initiator proteins for the assembly of the 30S subunit of the ribosome. The S9, S13, S19, S10, S14, and S3 subunits depend on S7 for assembly [Nowotny88, Grondek04, Bunner10]. The K35 residue of S7 appears to be required for efficient assembly [Fredrick00].

S7 crosslinks to the anticodon loop of tRNAs, indicating its location close to the decoding site of the ribosome [Podkowinski89, Rosen97]. S7 also crosslinks to mRNA [Stade89, Dontsova91]; the C-terminal region of S7 is the predominant crosslinking site [Greuer99]. S7 was also shown to crosslink to IF3 [MacKeen80, Cooperman81, Boileau83]. Footprinting of IF3 on 16S rRNA and modelling of IF3-30S subunit interactions suggested that IF3 is located near S7 and S11 [Dallas01]. S7 and S11 functionally interact [Robert03]. In addition, S7 is the major crosslinking target of the 4.5S RNA component of the signal recognition particle [Gu05].

S7 is a translational feedback repressor [Dean81], regulating the synthesis of itself and the other gene products encoded together with S7 in an operon: S12, S7, EF-G and possibly EF-Tu [Saito94a]. Independently expressed S7 is not subject to translational autoregulation; therefore, regulation of S7 is achieved through regulation of translation of S12 and translational coupling with S12 [Saito94a]. Two regions located between rpsL and rpsG interact with S7 and are important for S7-mediated repression [Saito94, Golovin06, Surdina08]. The same determinants of S7 that are responsible for binding 16S rRNA are also involved in binding to its own mRNA [Robert01].

The antibiotic puromycin can be crosslinked to an amino-terminal peptide of S7 [Bischof94]. A deletion that truncates the β-hairpin of S7, ΔR77-Y84, increases ribosomal frameshifting, indicating that the ribosomal E (exit) site plays a role in reading frame maintenance [Devaraj09].

Essentiality data for rpsG knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 30S ribosomal subunit: 30S ribosomal subunit protein S8

Synonyms: RpsH

Gene: rpsH Accession Numbers: EG10907 (EcoCyc), b3306, ECK3293

Locations: cytosol, ribosome

Sequence Length: 130 AAs

Molecular Weight: 14.127 kD (from nucleotide sequence)

Molecular Weight: 15.8 kD (experimental) [Tindall81]

GO Terms:

Biological Process: GO:0043488 - regulation of mRNA stability Inferred from experiment [Mattheakis89]
GO:0006412 - translation Inferred by computational analysis [GOA01]
GO:0006417 - regulation of translation Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0019843 - rRNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, Mizushima70]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022627 - cytosolic small ribosomal subunit Inferred from experiment [Hindennach71, WittmannLiebold73]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation
regulation type of regulation posttranscriptional

Unification Links: DIP:DIP-47901N , EcoliWiki:b3306 , Mint:MINT-1318565 , ModBase:P0A7W7 , PR:PRO_000023861 , Pride:P0A7W7 , Protein Model Portal:P0A7W7 , RefSeq:NP_417765 , SMR:P0A7W7 , String:511145.b3306 , UniProt:P0A7W7

Relationship Links: InterPro:IN-FAMILY:IPR000630 , Panther:IN-FAMILY:PTHR11758 , PDB:Structure:1EG0 , PDB:Structure:1M5G , PDB:Structure:1P6G , PDB:Structure:1P87 , PDB:Structure:1S03 , PDB:Structure:1VS5 , PDB:Structure:1VS7 , PDB:Structure:2AVY , PDB:Structure:2AW7 , PDB:Structure:2GY9 , PDB:Structure:2GYB , PDB:Structure:2I2P , PDB:Structure:2I2U , PDB:Structure:2QAL , PDB:Structure:2QAN , PDB:Structure:2QB9 , PDB:Structure:2QBB , PDB:Structure:2QBD , PDB:Structure:2QBF , PDB:Structure:2QBH , PDB:Structure:2QBJ , PDB:Structure:2QOU , PDB:Structure:2QOW , PDB:Structure:2QOY , PDB:Structure:2QP0 , PDB:Structure:2VHO , PDB:Structure:2VHP , PDB:Structure:2WWL , PDB:Structure:2YKR , PDB:Structure:2Z4K , PDB:Structure:2Z4M , PDB:Structure:3DF1 , PDB:Structure:3DF3 , PDB:Structure:3E1A , PDB:Structure:3E1C , PDB:Structure:3FIH , PDB:Structure:3I1M , PDB:Structure:3I1O , PDB:Structure:3I1Q , PDB:Structure:3I1S , PDB:Structure:3I1Z , PDB:Structure:3I21 , PDB:Structure:3IZV , PDB:Structure:3IZW , PDB:Structure:3J00 , PDB:Structure:3J0U , PDB:Structure:3J0V , PDB:Structure:3J0X , PDB:Structure:3J0Z , PDB:Structure:3J10 , PDB:Structure:3J13 , PDB:Structure:3J18 , PDB:Structure:3J36 , PDB:Structure:3KC4 , PDB:Structure:3OAQ , PDB:Structure:3OAR , PDB:Structure:3OFA , PDB:Structure:3OFB , PDB:Structure:3OFO , PDB:Structure:3OFP , PDB:Structure:3OFX , PDB:Structure:3OFY , PDB:Structure:3OR9 , PDB:Structure:3ORA , PDB:Structure:3SFS , PDB:Structure:3UOQ , PDB:Structure:4A2I , PDB:Structure:4ADV , PDB:Structure:4GAQ , PDB:Structure:4GAS , PDB:Structure:4GD1 , PDB:Structure:4GD2 , PDB:Structure:4KIY , PDB:Structure:4KJ0 , PDB:Structure:4KJ2 , PDB:Structure:4KJ4 , PDB:Structure:4KJ6 , PDB:Structure:4KJ8 , PDB:Structure:4KJA , PDB:Structure:4KJC , Pfam:IN-FAMILY:PF00410 , Prosite:IN-FAMILY:PS00053

Summary:
The S8 protein is a component of the 30S subunit of the ribosome and also functions in the post-transcriptional regulation of the ribosomal protein genes encoded in the spc operon.

The S8 protein binds to 16S rRNA [Schaup73] in the absence of other ribosomal proteins [Schaup70]. S8 binding is not absolutely required for assembly of the 30S ribosomal subunit platform, but it influences the organization of the 16S rRNA central domain [Jagannathan03]. Sites within 16S rRNA where S8 interacts have been determined [Wower83, Gregory84, Gregory86, Wiener88, Mougel93, Wu94], and the secondary and tertiary structure of the binding region has been investigated [Mougel87, Allmang94, Kalurachchi97, Kalurachchi98]. The unique cysteine residue present in S8 is essential for 16S rRNA binding [Mougel86], although it may not be involved in RNA recognition [Wu93]. Other sequence determinants important for 16S rRNA binding have been investigated [Wower92, Wu93, Moine97]. The affinity of S8 for 16S rRNA and thus the stability of the complex is correlated with the optimal growth temperature of various organisms [Gruber03].

In addition to its function in the ribosome, the ribosomal protein S8 binds to a site overlapping and sequestering the L5 initiation codon in the spc operon mRNA. It thereby represses initiation of L5 (rplE) translation [Thomas87, Dean81a, Yates80], and translational coupling ensures the coordinated regulation of genes downstream of rplE [Mattheakis88]. However, it is not known whether S8 also regulates the translation of the last two open reading frames of the spc operon, secY and rpmJ. Expression of the first two genes of the spc operon, encoding ribosomal proteins L14 and L24, is regulated by the same interaction of S8 with spc operon mRNA via "retroregulation" [Mattheakis89]. Processing of spc mRNA was shown to be stimulated by overproduction of S8 [Mattheakis88], and this effect is dependent on polynucleotide phosphorylase and RNase II [Mattheakis89].

The target site on mRNA for S8 feedback regulation shows structural similarity to the region of 16S rRNA that binds S8 [Olins81, Gregory88, Cerretti88]. The affinity of S8 for its mRNA binding site is approximately 5-fold lower than for its rRNA binding site due to differences in the secondary structure of the sites [Wu94]. A crystal structure of the complex between S8 and spc operon mRNA has been determined at 2.8 Å resolution and shows similarity to the structure of the S8/helix 21 complex in the small ribosomal subunit [Merianos04].

Essentiality data for rpsH knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 30S ribosomal subunit: 30S ribosomal subunit protein S9

Synonyms: RpsI

Gene: rpsI Accession Numbers: EG10908 (EcoCyc), b3230, ECK3219

Locations: cytosol, ribosome

Sequence Length: 130 AAs

Molecular Weight: 14.856 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA01]
Molecular Function: GO:0000049 - tRNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022627 - cytosolic small ribosomal subunit Inferred from experiment [Hindennach71]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-35799N , EcoliWiki:b3230 , Mint:MINT-1290939 , PR:PRO_000023862 , Pride:P0A7X3 , Protein Model Portal:P0A7X3 , RefSeq:NP_417697 , SMR:P0A7X3 , String:511145.b3230 , UniProt:P0A7X3

Relationship Links: InterPro:IN-FAMILY:IPR000754 , InterPro:IN-FAMILY:IPR014721 , InterPro:IN-FAMILY:IPR020568 , InterPro:IN-FAMILY:IPR020574 , InterPro:IN-FAMILY:IPR023035 , Panther:IN-FAMILY:PTHR21569 , PDB:Structure:1M5G , PDB:Structure:1P6G , PDB:Structure:1P87 , PDB:Structure:1VS5 , PDB:Structure:1VS7 , PDB:Structure:2AVY , PDB:Structure:2AW7 , PDB:Structure:2GY9 , PDB:Structure:2GYB , PDB:Structure:2I2P , PDB:Structure:2I2U , PDB:Structure:2QAL , PDB:Structure:2QAN , PDB:Structure:2QB9 , PDB:Structure:2QBB , PDB:Structure:2QBD , PDB:Structure:2QBF , PDB:Structure:2QBH , PDB:Structure:2QBJ , PDB:Structure:2QOU , PDB:Structure:2QOW , PDB:Structure:2QOY , PDB:Structure:2QP0 , PDB:Structure:2VHO , PDB:Structure:2VHP , PDB:Structure:2WWL , PDB:Structure:2YKR , PDB:Structure:2Z4K , PDB:Structure:2Z4M , PDB:Structure:3DF1 , PDB:Structure:3DF3 , PDB:Structure:3E1A , PDB:Structure:3E1C , PDB:Structure:3FIH , PDB:Structure:3I1M , PDB:Structure:3I1O , PDB:Structure:3I1Q , PDB:Structure:3I1S , PDB:Structure:3I1Z , PDB:Structure:3I21 , PDB:Structure:3IZV , PDB:Structure:3IZW , PDB:Structure:3J00 , PDB:Structure:3J0U , PDB:Structure:3J0V , PDB:Structure:3J0X , PDB:Structure:3J0Z , PDB:Structure:3J10 , PDB:Structure:3J13 , PDB:Structure:3J18 , PDB:Structure:3J36 , PDB:Structure:3KC4 , PDB:Structure:3OAQ , PDB:Structure:3OAR , PDB:Structure:3OFA , PDB:Structure:3OFB , PDB:Structure:3OFO , PDB:Structure:3OFP , PDB:Structure:3OFX , PDB:Structure:3OFY , PDB:Structure:3OR9 , PDB:Structure:3ORA , PDB:Structure:3SFS , PDB:Structure:3UOQ , PDB:Structure:4A2I , PDB:Structure:4ADV , PDB:Structure:4GAQ , PDB:Structure:4GAS , PDB:Structure:4GD1 , PDB:Structure:4GD2 , PDB:Structure:4KIY , PDB:Structure:4KJ0 , PDB:Structure:4KJ2 , PDB:Structure:4KJ4 , PDB:Structure:4KJ6 , PDB:Structure:4KJ8 , PDB:Structure:4KJA , PDB:Structure:4KJC , Pfam:IN-FAMILY:PF00380 , Prosite:IN-FAMILY:PS00360

Summary:
The S9 protein is a component of the 30S subunit of the ribosome.

S9 was shown to crosslink to domains 3 and 4 of 16S rRNA [Hajnsdorf86, Chiaruttini86] and increases protection against ribunuclease digestion of the hairpin loop 41 near the 3' terminus of 16S rRNA by a mixture containing S7, S14, and S19 [Wiener87]. The effect of S9 may be dependent on the presence of S14 [Wiener88]. S7 is required for and accelerates binding of S9 to the 16S rRNA [Bunner10]. S9 crosslinks to tRNA at the P site of the ribosome and weakly to tRNA at the A site [Osswald95]. The assembly cofactors Era, RimM and RimP accelerate the binding rate of S9 during 30S assembly [Bunner10a].

Structural modelling suggested that the C-terminal region of S9 interacts with the P-site tRNA. Studies with rpsI mutants lacking this region show that the C-terminal tail is not essential for the function of S9, but such mutants have slower growth rates. In vitro, deletion of the C-terminal tail of S9 affects binding of tRNAs with anticodon stem sequences that are most divergent from initiator tRNAs [Hoang04]. Deletion of three C terminal amino acids of S9 results in altered translation initiation from various codons [Arora13].

S9 is one of the subunits required for the ribosome-dependent GTPase activity of EF-G [Marsh73]. A decreased amount of S9 in the cell may cause a defect in ribosome maturation [Kaczanowska04].

An rpsI null mutant is viable, but has a slow growth phenotype [Bubunenko07, Shoji11].

Essentiality data for rpsI knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Indeterminate 37 Aerobic 7   No [Baba06, Comment 2]
Low [Bubunenko07]

Subunit of 30S ribosomal subunit: 30S ribosomal subunit protein S10

Synonyms: NusE, RpsJ

Gene: rpsJ Accession Numbers: EG10909 (EcoCyc), b3321, ECK3308

Locations: cytosol, ribosome

Sequence Length: 103 AAs

Molecular Weight: 11.736 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Zheng11, Arifuzzaman06, Mason92, Butland05]
GO:0000049 - tRNA binding Inferred by computational analysis [GOA06]
GO:0003723 - RNA binding Inferred by computational analysis [GOA01]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022627 - cytosolic small ribosomal subunit Inferred from experiment [Hindennach71, Hardy69]
GO:0005622 - intracellular Inferred by computational analysis [GOA01]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation
regulation type of regulation transcriptional level

Unification Links: DIP:DIP-35797N , EcoliWiki:b3321 , Mint:MINT-1283940 , ModBase:P0A7R5 , PR:PRO_000023863 , Pride:P0A7R5 , Protein Model Portal:P0A7R5 , RefSeq:NP_417780 , SMR:P0A7R5 , String:511145.b3321 , UniProt:P0A7R5

Relationship Links: InterPro:IN-FAMILY:IPR001848 , InterPro:IN-FAMILY:IPR018268 , InterPro:IN-FAMILY:IPR027486 , Panther:IN-FAMILY:PTHR11700 , PDB:Structure:1M5G , PDB:Structure:1P6G , PDB:Structure:1P87 , PDB:Structure:1VS5 , PDB:Structure:1VS7 , PDB:Structure:2AVY , PDB:Structure:2AW7 , PDB:Structure:2GY9 , PDB:Structure:2GYB , PDB:Structure:2I2P , PDB:Structure:2I2U , PDB:Structure:2KVQ , PDB:Structure:2QAL , PDB:Structure:2QAN , PDB:Structure:2QB9 , PDB:Structure:2QBB , PDB:Structure:2QBD , PDB:Structure:2QBF , PDB:Structure:2QBH , PDB:Structure:2QBJ , PDB:Structure:2QOU , PDB:Structure:2QOW , PDB:Structure:2QOY , PDB:Structure:2QP0 , PDB:Structure:2VHO , PDB:Structure:2VHP , PDB:Structure:2WWL , PDB:Structure:2YKR , PDB:Structure:2Z4K , PDB:Structure:2Z4M , PDB:Structure:3D3B , PDB:Structure:3D3C , PDB:Structure:3DF1 , PDB:Structure:3DF3 , PDB:Structure:3E1A , PDB:Structure:3E1C , PDB:Structure:3FIH , PDB:Structure:3I1M , PDB:Structure:3I1O , PDB:Structure:3I1Q , PDB:Structure:3I1S , PDB:Structure:3I1Z , PDB:Structure:3I21 , PDB:Structure:3IMQ , PDB:Structure:3IZV , PDB:Structure:3IZW , PDB:Structure:3J00 , PDB:Structure:3J0U , PDB:Structure:3J0V , PDB:Structure:3J0X , PDB:Structure:3J0Z , PDB:Structure:3J10 , PDB:Structure:3J13 , PDB:Structure:3J18 , PDB:Structure:3J36 , PDB:Structure:3KC4 , PDB:Structure:3OAQ , PDB:Structure:3OAR , PDB:Structure:3OFA , PDB:Structure:3OFB , PDB:Structure:3OFO , PDB:Structure:3OFP , PDB:Structure:3OFX , PDB:Structure:3OFY , PDB:Structure:3OR9 , PDB:Structure:3ORA , PDB:Structure:3SFS , PDB:Structure:3UOQ , PDB:Structure:4A2I , PDB:Structure:4ADV , PDB:Structure:4GAQ , PDB:Structure:4GAS , PDB:Structure:4GD1 , PDB:Structure:4GD2 , PDB:Structure:4KIY , PDB:Structure:4KJ0 , PDB:Structure:4KJ2 , PDB:Structure:4KJ4 , PDB:Structure:4KJ6 , PDB:Structure:4KJ8 , PDB:Structure:4KJA , PDB:Structure:4KJC , Pfam:IN-FAMILY:PF00338 , Prints:IN-FAMILY:PR00971 , Prosite:IN-FAMILY:PS00361

Summary:
The S10 protein (NusE) is a component of the 30S subunit of the ribosome and, in a complex with NusB, plays a role in transcription antitermination.

S10 can be crosslinked to tRNA in the ribosomal P site [Riehl82] and may contact 16S rRNA in two separate domains [Powers88].

S10 may be directly involved in the regulation of transcription termination [Das84, Warren84, Das85]. The nusE71 mutation in the rpsJ gene was first shown to affect regulation of transcription termination by the bacteriophage λ antiterminator N [Friedman81]. The nusE71 allele is a point mutation, changing a single amino acid, Ala86, to Asp. It is the only rpsJ allele known to have a Nus- phenotype [Court95]. The nusE71 mutation may be specific for λ antitermination; it appears to have no effect on boxA-mediated increase in the rate of transcription of rrn operons [Zellars99].

S10 is also suggested to function in rrn antitermination. S10 can form a heterodimer with NusB [Mason92]; the heterodimer can bind to the rrn boxA sequence [Nodwell93, Luttgen02]. Detailed analysis of the assembly pathway for the boxA-containing core antitermination complex has been performed [Greive05]. S10 was shown to bind RNA non-specifically and increases the affinity of NusB for boxA RNA [Greive05].

NusE: "N utilization substance E"

Reviews: [Squires00, Weisberg08]

Essentiality data for rpsJ knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 30S ribosomal subunit: 30S ribosomal subunit protein S11

Synonyms: RpsK

Gene: rpsK Accession Numbers: EG10910 (EcoCyc), b3297, ECK3284

Locations: cytosol, ribosome

Sequence Length: 129 AAs

Molecular Weight: 13.845 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0003735 - structural constituent of ribosome Inferred from experiment Inferred by computational analysis [GOA01, Hardy69]
GO:0070181 - small ribosomal subunit rRNA binding Inferred from experiment [Powers95a, Chiaruttini89]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022627 - cytosolic small ribosomal subunit Inferred from experiment [Hindennach71, Hardy69]
GO:0005622 - intracellular Inferred by computational analysis [GOA01]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-47838N , EcoliWiki:b3297 , Mint:MINT-1232137 , PR:PRO_000023864 , Pride:P0A7R9 , Protein Model Portal:P0A7R9 , RefSeq:NP_417756 , SMR:P0A7R9 , String:511145.b3297 , UniProt:P0A7R9

Relationship Links: InterPro:IN-FAMILY:IPR001971 , InterPro:IN-FAMILY:IPR018102 , InterPro:IN-FAMILY:IPR019981 , Panther:IN-FAMILY:PTHR11759 , PDB:Structure:1M5G , PDB:Structure:1P6G , PDB:Structure:1P87 , PDB:Structure:1VS5 , PDB:Structure:1VS7 , PDB:Structure:2AVY , PDB:Structure:2AW7 , PDB:Structure:2GY9 , PDB:Structure:2GYB , PDB:Structure:2I2P , PDB:Structure:2I2U , PDB:Structure:2QAL , PDB:Structure:2QAN , PDB:Structure:2QB9 , PDB:Structure:2QBB , PDB:Structure:2QBD , PDB:Structure:2QBF , PDB:Structure:2QBH , PDB:Structure:2QBJ , PDB:Structure:2QOU , PDB:Structure:2QOW , PDB:Structure:2QOY , PDB:Structure:2QP0 , PDB:Structure:2VHO , PDB:Structure:2VHP , PDB:Structure:2WWL , PDB:Structure:2YKR , PDB:Structure:2Z4K , PDB:Structure:2Z4M , PDB:Structure:3DF1 , PDB:Structure:3DF3 , PDB:Structure:3E1A , PDB:Structure:3E1C , PDB:Structure:3FIH , PDB:Structure:3I1M , PDB:Structure:3I1O , PDB:Structure:3I1Q , PDB:Structure:3I1S , PDB:Structure:3I1Z , PDB:Structure:3I21 , PDB:Structure:3IZV , PDB:Structure:3IZW , PDB:Structure:3J00 , PDB:Structure:3J0U , PDB:Structure:3J0V , PDB:Structure:3J0X , PDB:Structure:3J0Z , PDB:Structure:3J10 , PDB:Structure:3J13 , PDB:Structure:3J18 , PDB:Structure:3J36 , PDB:Structure:3KC4 , PDB:Structure:3OAQ , PDB:Structure:3OAR , PDB:Structure:3OFA , PDB:Structure:3OFB , PDB:Structure:3OFO , PDB:Structure:3OFP , PDB:Structure:3OFX , PDB:Structure:3OFY , PDB:Structure:3OR9 , PDB:Structure:3ORA , PDB:Structure:3SFS , PDB:Structure:3UOQ , PDB:Structure:4A2I , PDB:Structure:4ADV , PDB:Structure:4GAQ , PDB:Structure:4GAS , PDB:Structure:4GD1 , PDB:Structure:4GD2 , PDB:Structure:4KIY , PDB:Structure:4KJ0 , PDB:Structure:4KJ2 , PDB:Structure:4KJ4 , PDB:Structure:4KJ6 , PDB:Structure:4KJ8 , PDB:Structure:4KJA , PDB:Structure:4KJC , Pfam:IN-FAMILY:PF00411 , Prosite:IN-FAMILY:PS00054

Summary:
The S11 protein is a component of the 30S subunit of the ribosome.

S11 is a component of the ribosomal P site [Stern88] and crosslinks to a nucleotide in the D loop of tRNA [Rosen97]. S11 was also shown to crosslink to IF3 [MacKeen80, Cooperman81, Boileau83]. Footprinting of IF3 on 16S rRNA and modelling of IF3-30S subunit interactions suggested that IF3 is located near S7 and S11 [Dallas01].

S11, S6, and S18 interact cooperatively with two loop regions of 16S rRNA [Stern88]. S11 and S7 functionally interact [Robert03].

S11 is methylated at the amino terminal alanine residue [Arnold99] and contains isoaspartate [David99].

Essentiality data for rpsK knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 30S ribosomal subunit: 30S ribosomal subunit protein S12

Synonyms: StrA, AsuB, RpsL

Gene: rpsL Accession Numbers: EG10911 (EcoCyc), b3342, ECK3329

Locations: cytosol, ribosome

Sequence Length: 124 AAs

Molecular Weight: 13.737 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0000372 - Group I intron splicing Inferred from experiment [Coetzee94]
GO:0006412 - translation Inferred from experiment Inferred by computational analysis [GOA06, GOA01, Zengel77]
GO:0033120 - positive regulation of RNA splicing Inferred from experiment [Coetzee94]
GO:0034337 - RNA folding Inferred from experiment [Coetzee94]
GO:0046677 - response to antibiotic Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Zheng11, Hauser14]
GO:0019843 - rRNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA06, Stern88]
GO:0034336 - misfolded RNA binding Inferred from experiment [Coetzee94]
GO:0000049 - tRNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Zhang07]
GO:0022627 - cytosolic small ribosomal subunit Inferred from experiment [Hindennach71, WittmannLiebold73, Kaltschmidt70]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0015935 - small ribosomal subunit Inferred by computational analysis [GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-35806N , DisProt:DP00145 , EcoliWiki:b3342 , PR:PRO_000023865 , Pride:P0A7S3 , Protein Model Portal:P0A7S3 , RefSeq:NP_417801 , SMR:P0A7S3 , String:511145.b3342 , UniProt:P0A7S3

Relationship Links: InterPro:IN-FAMILY:IPR005679 , InterPro:IN-FAMILY:IPR006032 , InterPro:IN-FAMILY:IPR012340 , Panther:IN-FAMILY:PTHR11652 , PDB:Structure:1M5G , PDB:Structure:1MJ1 , PDB:Structure:1P6G , PDB:Structure:1P87 , PDB:Structure:1VS5 , PDB:Structure:1VS7 , PDB:Structure:1ZN1 , PDB:Structure:2AVY , PDB:Structure:2AW7 , PDB:Structure:2GY9 , PDB:Structure:2GYB , PDB:Structure:2I2P , PDB:Structure:2I2U , PDB:Structure:2QAL , PDB:Structure:2QAN , PDB:Structure:2QB9 , PDB:Structure:2QBB , PDB:Structure:2QBD , PDB:Structure:2QBF , PDB:Structure:2QBH , PDB:Structure:2QBJ , PDB:Structure:2QOU , PDB:Structure:2QOW , PDB:Structure:2QOY , PDB:Structure:2QP0 , PDB:Structure:2VHO , PDB:Structure:2VHP , PDB:Structure:2WWL , PDB:Structure:2YKR , PDB:Structure:2Z4K , PDB:Structure:2Z4M , PDB:Structure:3DEG , PDB:Structure:3DF1 , PDB:Structure:3DF3 , PDB:Structure:3E1A , PDB:Structure:3E1C , PDB:Structure:3EP2 , PDB:Structure:3EQ3 , PDB:Structure:3EQ4 , PDB:Structure:3FIH , PDB:Structure:3I1M , PDB:Structure:3I1O , PDB:Structure:3I1Q , PDB:Structure:3I1S , PDB:Structure:3I1Z , PDB:Structure:3I21 , PDB:Structure:3IZV , PDB:Structure:3IZW , PDB:Structure:3J00 , PDB:Structure:3J0D , PDB:Structure:3J0E , PDB:Structure:3J0U , PDB:Structure:3J0V , PDB:Structure:3J0X , PDB:Structure:3J0Z , PDB:Structure:3J10 , PDB:Structure:3J13 , PDB:Structure:3J18 , PDB:Structure:3J36 , PDB:Structure:3KC4 , PDB:Structure:3OAQ , PDB:Structure:3OAR , PDB:Structure:3OFA , PDB:Structure:3OFB , PDB:Structure:3OFO , PDB:Structure:3OFP , PDB:Structure:3OFX , PDB:Structure:3OFY , PDB:Structure:3OR9 , PDB:Structure:3ORA , PDB:Structure:3SFS , PDB:Structure:3UOQ , PDB:Structure:4A2I , PDB:Structure:4ADV , PDB:Structure:4GAQ , PDB:Structure:4GAS , PDB:Structure:4GD1 , PDB:Structure:4GD2 , PDB:Structure:4KIY , PDB:Structure:4KJ0 , PDB:Structure:4KJ2 , PDB:Structure:4KJ4 , PDB:Structure:4KJ6 , PDB:Structure:4KJ8 , PDB:Structure:4KJA , PDB:Structure:4KJC , Pfam:IN-FAMILY:PF00164 , Prints:IN-FAMILY:PR01034 , Prosite:IN-FAMILY:PS00055

Summary:
The S12 protein is a component of the 30S subunit of the ribosome and plays a role in translational accuracy.

Certain mutations in S12 cause streptomycin resistance [Ozaki69]. The streptomycin resistance phenotype is recessive [Lederberg51]. Some mutations causing streptomycin resistance also lead to higher translational accuracy [Yates77, Bouadloun83] and a lower rate of protein chain elongation [Zengel77]. The mutations appear to exert their effect by altering the structure of 16S rRNA [Allen89]. Both S12 and S5 appear to facilitate changes in 16S rRNA structure during translation [Lodmell97]. S12 influences the selection of aminoacyl-tRNAs and discrimination both before and after GTP hydrolysis [Yates79], which may be explained by its influence on P site binding of charged tRNAs [Karimi96]. S12 and S13 are also thought to be involved in maintenance of the pre-translocation state of the ribosome [Cukras03]. The kinetic properties of ribosomes with various mutant forms of S12 have been investigated [Bilgin92].

S12 was shown to crosslink to IF3 [Hawley74, MacKeen80, Cooperman81], IF1 [Boileau83] and EF-G [Girshovich81] and protects the pseudoknot structure of the 530 stem/loop region [Powers91], the 900 stem/loop region and the 5' terminus of the 16S rRNA [Stern88] from chemical probes. S12 functionally interacts with the 1409-1491 region [OConnor91, VilaSanjurjo07], the 912 region [VilaSanjurjo07], and G530 [Powers94] of 16S rRNA as well as the base at position 2661 in 23S rRNA [Tapio91]. The Tyr116-Lys119 residues of S12 appear to be located near the peptidyl transferase center of the ribosome [Bischof95].

S12 can bind RNA with broad specificity and act as an RNA chaperone in vitro [Coetzee94], although only weakly in vivo [Clodi99]. S12 is thought to stimulate splicing of Group I introns by resolving misfolded RNAs and assisting proper folding [Coetzee94]. S12 was found to be required for efficient splicing of the phage T4 td gene in vivo [Semrad98].

S12 contains a β-methylthio modification at the Asp88 residue of the mature protein [Kowalak96, Arnold99]. The enzyme responsible for this modification, RimO, has been identified [Anton08].

AsuB: "antisuppressor mutation" [Sullivan85]

Essentiality data for rpsL knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 30S ribosomal subunit: 30S ribosomal subunit protein S13

Synonyms: RpsM

Gene: rpsM Accession Numbers: EG10912 (EcoCyc), b3298, ECK3285

Locations: cytosol, ribosome

Sequence Length: 118 AAs

Molecular Weight: 13.099 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
GO:0042254 - ribosome biogenesis Inferred by computational analysis [Gaudet10]
Molecular Function: GO:0000049 - tRNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
GO:0003676 - nucleic acid binding Inferred by computational analysis [GOA01]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022627 - cytosolic small ribosomal subunit Inferred from experiment [Hindennach71, WittmannLiebold73]
GO:0005622 - intracellular Inferred by computational analysis [GOA01]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-35855N , EcoliWiki:b3298 , Mint:MINT-1290225 , PR:PRO_000023866 , Pride:P0A7S9 , Protein Model Portal:P0A7S9 , RefSeq:NP_417757 , SMR:P0A7S9 , String:511145.b3298 , UniProt:P0A7S9

Relationship Links: InterPro:IN-FAMILY:IPR001892 , InterPro:IN-FAMILY:IPR010979 , InterPro:IN-FAMILY:IPR018269 , InterPro:IN-FAMILY:IPR019980 , InterPro:IN-FAMILY:IPR027437 , Panther:IN-FAMILY:PTHR10871 , PDB:Structure:1M5G , PDB:Structure:1P6G , PDB:Structure:1P87 , PDB:Structure:1VS5 , PDB:Structure:1VS7 , PDB:Structure:2AVY , PDB:Structure:2AW7 , PDB:Structure:2GY9 , PDB:Structure:2GYB , PDB:Structure:2I2P , PDB:Structure:2I2U , PDB:Structure:2QAL , PDB:Structure:2QAN , PDB:Structure:2QB9 , PDB:Structure:2QBB , PDB:Structure:2QBD , PDB:Structure:2QBF , PDB:Structure:2QBH , PDB:Structure:2QBJ , PDB:Structure:2QOU , PDB:Structure:2QOW , PDB:Structure:2QOY , PDB:Structure:2QP0 , PDB:Structure:2VHO , PDB:Structure:2VHP , PDB:Structure:2WWL , PDB:Structure:2YKR , PDB:Structure:2Z4K , PDB:Structure:2Z4M , PDB:Structure:3DF1 , PDB:Structure:3DF3 , PDB:Structure:3E1A , PDB:Structure:3E1C , PDB:Structure:3FIH , PDB:Structure:3I1M , PDB:Structure:3I1O , PDB:Structure:3I1Q , PDB:Structure:3I1S , PDB:Structure:3I1Z , PDB:Structure:3I21 , PDB:Structure:3IZV , PDB:Structure:3IZW , PDB:Structure:3J00 , PDB:Structure:3J0U , PDB:Structure:3J0V , PDB:Structure:3J0X , PDB:Structure:3J0Z , PDB:Structure:3J10 , PDB:Structure:3J13 , PDB:Structure:3J18 , PDB:Structure:3J36 , PDB:Structure:3KC4 , PDB:Structure:3OAQ , PDB:Structure:3OAR , PDB:Structure:3OFA , PDB:Structure:3OFB , PDB:Structure:3OFO , PDB:Structure:3OFP , PDB:Structure:3OFX , PDB:Structure:3OFY , PDB:Structure:3OR9 , PDB:Structure:3ORA , PDB:Structure:3SFS , PDB:Structure:3UOQ , PDB:Structure:4A2I , PDB:Structure:4ADV , PDB:Structure:4GAQ , PDB:Structure:4GAS , PDB:Structure:4GD1 , PDB:Structure:4GD2 , PDB:Structure:4KIY , PDB:Structure:4KJ0 , PDB:Structure:4KJ2 , PDB:Structure:4KJ4 , PDB:Structure:4KJ6 , PDB:Structure:4KJ8 , PDB:Structure:4KJA , PDB:Structure:4KJC , Pfam:IN-FAMILY:PF00416 , Prosite:IN-FAMILY:PS00646 , Prosite:IN-FAMILY:PS50159

Summary:
The S13 protein is a component of the 30S subunit of the ribosome, playing a key role in subunit association and the fidelity of translocation. The crystal structure of the ribosome [Schuwirth05], cryo-EM reconstructions [Gao03a], and crosslinking experiments [Lambert81] show that the S13 protein contacts the L5 protein of the large subunit of the ribosome.

S13 is thought to be involved in maintenance of pre-translocation state [Cukras03, Cukras05]. In vitro, a small subunit of the ribosome lacking S13 associates only poorly with the large subunit; the presence of tRNA and mRNA in the assay restores 70S complex formation [Cukras05]. In the absence of S13, initiation complex formation is defective [Cukras05], and the ribosome shows increased rates of factor-independent translocation [Cukras05]. In vivo, lack of S13 causes a deficit in polysome formation and the appearance of abundant free 30S and 50S subunits [Cukras05]. Ribosome modulation factor binds near S13, L2, and L13 [Yoshida02].

S13 forms a complex with S19 in order to bind to 16S rRNA at its specific site [Dijk77, Pohl88]. The C-terminal domain of S13 is primarily responsible for rRNA binding; its N-terminal domain may be responsible for association with S19 [Schwarzbauer85]. S13 can be crosslinked to 16S rRNA [Hajnsdorf86, Osswald87]; the sites of interaction have been identified by hydroxyl radical probing [Powers88, Powers95a, Heilek96a]. S13 crosslinks to tRNA at the P site of the ribosome and weakly to tRNA at the A site [Osswald95]. Structural modelling suggested that the C-terminal region of S13 interacts with the P-site tRNA. Studies with rpsM mutants lacking this region show that the C-terminal tail is not essential for the function of S13, but such mutants have slower growth rates. In vitro, deletion of the C-terminal tail of S13 causes a lower affinity of the 30S subunit for tRNAs [Hoang04].

S13 was also shown to crosslink to IF2 and IF3 [Boileau83]

rpsM is not essential for viability of E. coli, but an rpsM deletion strain has a severe growth defect [Cukras05]. An S13 mutant decreases in vivo translation efficiency and acts as antisuppressor of some suppressor tRNAs [Faxen94]. Suppressors of rimM point and deletion mutations localize to the C terminus of S13 [Bylund97, Lovgren04].

Essentiality data for rpsM knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Indeterminate 37 Aerobic 7   No [Baba06, Comment 2]
Low [Bubunenko07]

Subunit of 30S ribosomal subunit: 30S ribosomal subunit protein S14

Synonyms: RpsN

Gene: rpsN Accession Numbers: EG10913 (EcoCyc), b3307, ECK3294

Locations: cytosol, ribosome

Sequence Length: 101 AAs

Molecular Weight: 11.58 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [GOA06]
Cellular Component: GO:0022627 - cytosolic small ribosomal subunit Inferred from experiment [Hindennach71, WittmannLiebold73]
GO:0005622 - intracellular Inferred by computational analysis [GOA01]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-35805N , EcoliWiki:b3307 , Mint:MINT-1295909 , PR:PRO_000023867 , Pride:P0AG59 , Protein Model Portal:P0AG59 , RefSeq:NP_417766 , SMR:P0AG59 , String:511145.b3307 , Swiss-Model:P0AG59 , UniProt:P0AG59

Relationship Links: InterPro:IN-FAMILY:IPR001209 , InterPro:IN-FAMILY:IPR018271 , InterPro:IN-FAMILY:IPR023036 , Panther:IN-FAMILY:PTHR19836 , PDB:Structure:1M5G , PDB:Structure:1P6G , PDB:Structure:1P87 , PDB:Structure:1VS5 , PDB:Structure:1VS7 , PDB:Structure:2AVY , PDB:Structure:2AW7 , PDB:Structure:2GY9 , PDB:Structure:2GYB , PDB:Structure:2I2P , PDB:Structure:2I2U , PDB:Structure:2QAL , PDB:Structure:2QAN , PDB:Structure:2QB9 , PDB:Structure:2QBB , PDB:Structure:2QBD , PDB:Structure:2QBF , PDB:Structure:2QBH , PDB:Structure:2QBJ , PDB:Structure:2QOU , PDB:Structure:2QOW , PDB:Structure:2QOY , PDB:Structure:2QP0 , PDB:Structure:2VHO , PDB:Structure:2VHP , PDB:Structure:2WWL , PDB:Structure:2YKR , PDB:Structure:2Z4K , PDB:Structure:2Z4M , PDB:Structure:3DF1 , PDB:Structure:3DF3 , PDB:Structure:3E1A , PDB:Structure:3E1C , PDB:Structure:3FIH , PDB:Structure:3I1M , PDB:Structure:3I1O , PDB:Structure:3I1Q , PDB:Structure:3I1S , PDB:Structure:3I1Z , PDB:Structure:3I21 , PDB:Structure:3IZV , PDB:Structure:3IZW , PDB:Structure:3J00 , PDB:Structure:3J0U , PDB:Structure:3J0V , PDB:Structure:3J0X , PDB:Structure:3J0Z , PDB:Structure:3J10 , PDB:Structure:3J13 , PDB:Structure:3J18 , PDB:Structure:3J36 , PDB:Structure:3KC4 , PDB:Structure:3OAQ , PDB:Structure:3OAR , PDB:Structure:3OFA , PDB:Structure:3OFB , PDB:Structure:3OFO , PDB:Structure:3OFP , PDB:Structure:3OFX , PDB:Structure:3OFY , PDB:Structure:3OR9 , PDB:Structure:3ORA , PDB:Structure:3SFS , PDB:Structure:3UOQ , PDB:Structure:4A2I , PDB:Structure:4ADV , PDB:Structure:4GAQ , PDB:Structure:4GAS , PDB:Structure:4GD1 , PDB:Structure:4GD2 , PDB:Structure:4KIY , PDB:Structure:4KJ0 , PDB:Structure:4KJ2 , PDB:Structure:4KJ4 , PDB:Structure:4KJ6 , PDB:Structure:4KJ8 , PDB:Structure:4KJA , PDB:Structure:4KJC , Pfam:IN-FAMILY:PF00253 , Prosite:IN-FAMILY:PS00527

Summary:
The S14 protein is a component of the 30S subunit of the ribosome.

S14 has a role in tRNA binding [Graifer89, Kerlavage86]. S14 is photoaffinity labeled by puromycin, an analog of the 3' end of aminoacylated tRNA [Jaynes78, Weitzmann85, Bischof94]. S14 may be required for in vitro assembly of the small subunit [Ramakrishnan86].

A mixture containing S7, S14, and S19 protects the hairpin loop 41 near the 3' terminus of 16S rRNA against ribunuclease digestion [Wiener87]. The sites of interaction of S14 with 16S rRNA have been identified by hydroxyl radical probing [Powers88].

An amber mutation in rpsN exerts a polar effect on the genes distal to the rpsN gene in the spc operon [Cabezon80].

Essentiality data for rpsN knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 30S ribosomal subunit: 30S ribosomal subunit protein S15

Synonyms: SecC, RpsO

Gene: rpsO Accession Numbers: EG10914 (EcoCyc), b3165, ECK3154

Locations: cytosol, ribosome

Sequence Length: 89 AAs

Molecular Weight: 10.269 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006378 - mRNA polyadenylation Inferred from experiment [Hajnsdorf95]
GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0019843 - rRNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA06, Mizushima70]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022627 - cytosolic small ribosomal subunit Inferred from experiment [Hindennach71, WittmannLiebold73]
GO:0005622 - intracellular Inferred by computational analysis [GOA01]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-47909N , EcoliWiki:b3165 , Mint:MINT-1299353 , PR:PRO_000023868 , Pride:P0ADZ4 , Protein Model Portal:P0ADZ4 , RefSeq:NP_417634 , SMR:P0ADZ4 , String:511145.b3165 , Swiss-Model:P0ADZ4 , UniProt:P0ADZ4

Relationship Links: InterPro:IN-FAMILY:IPR000589 , InterPro:IN-FAMILY:IPR005290 , InterPro:IN-FAMILY:IPR009068 , Panther:IN-FAMILY:PTHR23321:SF10 , PDB:Structure:1EG0 , PDB:Structure:1P6G , PDB:Structure:1P87 , PDB:Structure:2AVY , PDB:Structure:2AW7 , PDB:Structure:2GY9 , PDB:Structure:2GYB , PDB:Structure:2QAL , PDB:Structure:2QAN , PDB:Structure:2QB9 , PDB:Structure:2QBB , PDB:Structure:2QBD , PDB:Structure:2QBF , PDB:Structure:2QBH , PDB:Structure:2QBJ , PDB:Structure:2QOU , PDB:Structure:2QOW , PDB:Structure:2QOY , PDB:Structure:2QP0 , PDB:Structure:2VAZ , PDB:Structure:2WWL , PDB:Structure:2YKR , PDB:Structure:2Z4K , PDB:Structure:2Z4M , PDB:Structure:3DF1 , PDB:Structure:3DF3 , PDB:Structure:3E1A , PDB:Structure:3E1C , PDB:Structure:3FIH , PDB:Structure:3I1M , PDB:Structure:3I1O , PDB:Structure:3I1Q , PDB:Structure:3I1S , PDB:Structure:3I1Z , PDB:Structure:3I21 , PDB:Structure:3IZV , PDB:Structure:3IZW , PDB:Structure:3J00 , PDB:Structure:3J18 , PDB:Structure:3J36 , PDB:Structure:3KC4 , PDB:Structure:3OAQ , PDB:Structure:3OAR , PDB:Structure:3OFA , PDB:Structure:3OFB , PDB:Structure:3OFO , PDB:Structure:3OFP , PDB:Structure:3OFX , PDB:Structure:3OFY , PDB:Structure:3OR9 , PDB:Structure:3ORA , PDB:Structure:3SFS , PDB:Structure:3UOQ , PDB:Structure:4A2I , PDB:Structure:4ADV , PDB:Structure:4GAQ , PDB:Structure:4GAS , PDB:Structure:4GD1 , PDB:Structure:4GD2 , PDB:Structure:4KIY , PDB:Structure:4KJ0 , PDB:Structure:4KJ2 , PDB:Structure:4KJ4 , PDB:Structure:4KJ6 , PDB:Structure:4KJ8 , PDB:Structure:4KJA , PDB:Structure:4KJC , Pfam:IN-FAMILY:PF00312 , Prosite:IN-FAMILY:PS00362

Summary:
The S15 protein is a component of the 30S subunit of the ribosome and also functions in the post-transcriptional regulation of its own expression.

The S15 protein binds to 16S rRNA in the absence of other ribosomal proteins [Zimmermann72, Zimmermann75, Gregory84]. Nucleotides essential for the S15-16S rRNA interaction have been determined by mutagenesis [Stark84, Serganov01] and nuclease protection [Wiener88, Mougel88]. Binding of S8 to 16S rRNA influences the central domain organisation and affects the rRNA environment of S15 [Jagannathan03].

In addition to its function in the ribosome, the ribosomal protein S15 binds to its own mRNA, stabilizing a pseudoknot secondary structure and impeding translation initiation [Portier90, Philippe90, Portier90a, Philippe94, Benard94, Philippe95, Benard98]. S15 appears to prevent the formation of a functional ternary 30S-mRNA-tRNA(fMet) complex, trapping the ribosome in a preinitiation complex [Philippe93]. rpsO mRNA and 16S rRNA compete for binding to S15 [Philippe94]; common structural determinants between the mRNA and rRNA bindig sites have been investigated, showing that there is limited similarity between the two targets [Serganov02, Mathy04].

Ribosomes lacking S15 can suppress the rpoH11 mutation [Yano89]. A mutation in rpsO (secC) suppresses a secA(Ts) allele [FerroNovick84]. S15 appears to be required for the optimal synthesis of lipoprotein [Watanabe88].

Processing and degradation of rpsO mRNA have been studied extensively; see for example [Le02a, Marujo03, Folichon03, Folichon05] and references therein.

Reviews: [Ehresmann95, Springer03]

Essentiality data for rpsO knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Indeterminate 37 Aerobic 7   No [Baba06, Yamamoto09]
Low [Bubunenko07]

Subunit of 30S ribosomal subunit: 30S ribosomal subunit protein S16

Synonyms: RpsP

Gene: rpsP Accession Numbers: EG10915 (EcoCyc), b2609, ECK2606

Locations: cytosol, ribosome

Sequence Length: 82 AAs

Molecular Weight: 9.191 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0000028 - ribosomal small subunit assembly Inferred from experiment [Ramaswamy09a]
GO:0000737 - DNA catabolic process, endonucleolytic Inferred from experiment [Oberto96]
GO:0006412 - translation Inferred by computational analysis [GOA01]
GO:0090305 - nucleic acid phosphodiester bond hydrolysis Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0004520 - endodeoxyribonuclease activity Inferred from experiment [Oberto96]
GO:0043566 - structure-specific DNA binding Inferred from experiment [Bonnefoy97]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0004518 - nuclease activity Inferred by computational analysis [UniProtGOA11]
GO:0004519 - endonuclease activity Inferred by computational analysis [UniProtGOA11]
GO:0016787 - hydrolase activity Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0022627 - cytosolic small ribosomal subunit Inferred from experiment [Hindennach71, WittmannLiebold73]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-47829N , EcoliWiki:b2609 , Mint:MINT-1280042 , ModBase:P0A7T3 , PR:PRO_000023869 , Pride:P0A7T3 , Protein Model Portal:P0A7T3 , RefSeq:NP_417100 , SMR:P0A7T3 , String:511145.b2609 , UniProt:P0A7T3

Relationship Links: InterPro:IN-FAMILY:IPR000307 , InterPro:IN-FAMILY:IPR020592 , InterPro:IN-FAMILY:IPR023803 , Panther:IN-FAMILY:PTHR12919 , PDB:Structure:1M5G , PDB:Structure:1ML5 , PDB:Structure:1P6G , PDB:Structure:1P87 , PDB:Structure:1VS5 , PDB:Structure:1VS7 , PDB:Structure:2AVY , PDB:Structure:2AW7 , PDB:Structure:2GY9 , PDB:Structure:2GYB , PDB:Structure:2I2P , PDB:Structure:2I2U , PDB:Structure:2QAL , PDB:Structure:2QAN , PDB:Structure:2QB9 , PDB:Structure:2QBB , PDB:Structure:2QBD , PDB:Structure:2QBF , PDB:Structure:2QBH , PDB:Structure:2QBJ , PDB:Structure:2QOU , PDB:Structure:2QOW , PDB:Structure:2QOY , PDB:Structure:2QP0 , PDB:Structure:2VHO , PDB:Structure:2VHP , PDB:Structure:2WWL , PDB:Structure:2YKR , PDB:Structure:2Z4K , PDB:Structure:2Z4M , PDB:Structure:3DF1 , PDB:Structure:3DF3 , PDB:Structure:3E1A , PDB:Structure:3E1C , PDB:Structure:3FIH , PDB:Structure:3I1M , PDB:Structure:3I1O , PDB:Structure:3I1Q , PDB:Structure:3I1S , PDB:Structure:3I1Z , PDB:Structure:3I21 , PDB:Structure:3IZV , PDB:Structure:3IZW , PDB:Structure:3J00 , PDB:Structure:3J0U , PDB:Structure:3J0V , PDB:Structure:3J0X , PDB:Structure:3J0Z , PDB:Structure:3J10 , PDB:Structure:3J13 , PDB:Structure:3J18 , PDB:Structure:3J36 , PDB:Structure:3KC4 , PDB:Structure:3OAQ , PDB:Structure:3OAR , PDB:Structure:3OFA , PDB:Structure:3OFB , PDB:Structure:3OFO , PDB:Structure:3OFP , PDB:Structure:3OFX , PDB:Structure:3OFY , PDB:Structure:3OR9 , PDB:Structure:3ORA , PDB:Structure:3SFS , PDB:Structure:3UOQ , PDB:Structure:4A2I , PDB:Structure:4ADV , PDB:Structure:4GAQ , PDB:Structure:4GAS , PDB:Structure:4GD1 , PDB:Structure:4GD2 , PDB:Structure:4KIY , PDB:Structure:4KJ0 , PDB:Structure:4KJ2 , PDB:Structure:4KJ4 , PDB:Structure:4KJ6 , PDB:Structure:4KJ8 , PDB:Structure:4KJA , PDB:Structure:4KJC , Pfam:IN-FAMILY:PF00886 , Prosite:IN-FAMILY:PS00732

Summary:
The S16 protein is a component of the 30S subunit of the ribosome and is essential for viability [Persson95].

S16 was also shown to be a DNA-binding protein with Mg2+-Mn2+-dependent endonuclease activity [Oberto96]. S16 preferentially binds to cruciform DNA structures; its endonuclease activity appears to be sequence-specific [Bonnefoy97].

S16 interacts with the 5' domain of 16S rRNA [Stern88a, Weitzmann93]. Binding of S16 to 16S rRNA is dependent on prior binding of S4 and S20 [Held74]. Subsequent binding of S16 suppresses non-native assembly intermediates and drives a conformational switch at helix 3 of 16S rRNA, stabilizing the decoding center of the 30S subunit [Ramaswamy09a].

S16 may bind Zn2+ [Katayama02].

Expression of rpsP is induced 16-fold upon exposure of cells to the biocide polyhexamethylene biguanide [Allen06].

Essentiality data for rpsP knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 30S ribosomal subunit: 30S ribosomal subunit protein S17

Synonyms: NeaA, RpsQ

Gene: rpsQ Accession Numbers: EG10916 (EcoCyc), b3311, ECK3298

Locations: cytosol, ribosome

Sequence Length: 84 AAs

Molecular Weight: 9.704 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0046677 - response to antibiotic Inferred from experiment Inferred by computational analysis [UniProtGOA11, Bollen75]
GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0019843 - rRNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA06, Held74]
GO:0070181 - small ribosomal subunit rRNA binding Inferred from experiment [Held74]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
Cellular Component: GO:0022627 - cytosolic small ribosomal subunit Inferred from experiment [Hindennach71, WittmannLiebold73]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-47952N , DisProt:DP00242 , EcoliWiki:b3311 , PR:PRO_000023870 , Pride:P0AG63 , Protein Model Portal:P0AG63 , RefSeq:NP_417770 , SMR:P0AG63 , String:511145.b3311 , Swiss-Model:P0AG63 , UniProt:P0AG63

Relationship Links: InterPro:IN-FAMILY:IPR000266 , InterPro:IN-FAMILY:IPR012340 , InterPro:IN-FAMILY:IPR019979 , InterPro:IN-FAMILY:IPR019984 , Panther:IN-FAMILY:PTHR10744 , PDB:Structure:1EG0 , PDB:Structure:1M5G , PDB:Structure:1P6G , PDB:Structure:1P87 , PDB:Structure:1VS5 , PDB:Structure:1VS7 , PDB:Structure:2AVY , PDB:Structure:2AW7 , PDB:Structure:2GY9 , PDB:Structure:2GYB , PDB:Structure:2I2P , PDB:Structure:2I2U , PDB:Structure:2QAL , PDB:Structure:2QAN , PDB:Structure:2QB9 , PDB:Structure:2QBB , PDB:Structure:2QBD , PDB:Structure:2QBF , PDB:Structure:2QBH , PDB:Structure:2QBJ , PDB:Structure:2QOU , PDB:Structure:2QOW , PDB:Structure:2QOY , PDB:Structure:2QP0 , PDB:Structure:2WWL , PDB:Structure:2YKR , PDB:Structure:2Z4K , PDB:Structure:2Z4M , PDB:Structure:3E1A , PDB:Structure:3E1C , PDB:Structure:3FIH , PDB:Structure:3I1M , PDB:Structure:3I1O , PDB:Structure:3I1Q , PDB:Structure:3I1S , PDB:Structure:3I1Z , PDB:Structure:3I21 , PDB:Structure:3IZV , PDB:Structure:3IZW , PDB:Structure:3J00 , PDB:Structure:3J0U , PDB:Structure:3J0V , PDB:Structure:3J0X , PDB:Structure:3J0Z , PDB:Structure:3J10 , PDB:Structure:3J13 , PDB:Structure:3J18 , PDB:Structure:3J36 , PDB:Structure:3KC4 , PDB:Structure:3OAQ , PDB:Structure:3OAR , PDB:Structure:3OFA , PDB:Structure:3OFB , PDB:Structure:3OFO , PDB:Structure:3OFP , PDB:Structure:3OFX , PDB:Structure:3OFY , PDB:Structure:3OR9 , PDB:Structure:3ORA , PDB:Structure:3SFS , PDB:Structure:3UOQ , PDB:Structure:4A2I , PDB:Structure:4ADV , PDB:Structure:4GAQ , PDB:Structure:4GAS , PDB:Structure:4GD1 , PDB:Structure:4GD2 , PDB:Structure:4KIY , PDB:Structure:4KJ0 , PDB:Structure:4KJ2 , PDB:Structure:4KJ4 , PDB:Structure:4KJ6 , PDB:Structure:4KJ8 , PDB:Structure:4KJA , PDB:Structure:4KJC , Pfam:IN-FAMILY:PF00366 , Prints:IN-FAMILY:PR00973 , ProDom:IN-FAMILY:PD001295 , Prosite:IN-FAMILY:PS00056

Summary:
The S17 protein is a component of the 30S subunit of the ribosome.

S17 binds directly to the 5' domain of 16S rRNA [Stern88a, Held74, Weitzmann93, Epe82, Wiener88]. Specific contact sites have been identified [Urlaub95, Urlaub97]. S17 can also be crosslinked to tRNA in the A site [Graifer89].

The initiating methionine of S17 is cleaved [Wasinger98, Arnold99].

A conditionally lethal point mutation in rpsQ leads to impaired assembly of the 30S ribosomal subunit [Herzog79]. Strains carrying the neaA301 allele of rpsQ exhibit neamine resistance [Bollen75] and increased misreading by the ribosome in vitro [Topisirovic77].

NeaA: "neamine resistance" [Bollen75]

Essentiality data for rpsQ knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Indeterminate 37 Aerobic 7   No [Baba06, Comment 2]
Low [Bubunenko07]

Subunit of 30S ribosomal subunit: 30S ribosomal subunit protein S18

Synonyms: RpsR

Gene: rpsR Accession Numbers: EG10917 (EcoCyc), b4202, ECK4198

Locations: cytosol, ribosome

Sequence Length: 75 AAs

Molecular Weight: 8.986 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Hauser14, Rajagopala14]
GO:0048027 - mRNA 5'-UTR binding Inferred from experiment [Matelska13]
GO:0070181 - small ribosomal subunit rRNA binding Inferred from experiment [Gregory84]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022627 - cytosolic small ribosomal subunit Inferred from experiment [Hindennach71]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-47889N , DisProt:DP00146 , EcoliWiki:b4202 , Mint:MINT-1247424 , ModBase:P0A7T7 , PR:PRO_000023871 , Pride:P0A7T7 , Protein Model Portal:P0A7T7 , RefSeq:NP_418623 , SMR:P0A7T7 , String:511145.b4202 , UniProt:P0A7T7

Relationship Links: InterPro:IN-FAMILY:IPR001648 , InterPro:IN-FAMILY:IPR018275 , Panther:IN-FAMILY:PTHR13479 , PDB:Structure:1M5G , PDB:Structure:1P6G , PDB:Structure:1P87 , PDB:Structure:1VS5 , PDB:Structure:1VS7 , PDB:Structure:2AVY , PDB:Structure:2AW7 , PDB:Structure:2GY9 , PDB:Structure:2GYB , PDB:Structure:2I2P , PDB:Structure:2I2U , PDB:Structure:2QAL , PDB:Structure:2QAN , PDB:Structure:2QB9 , PDB:Structure:2QBB , PDB:Structure:2QBD , PDB:Structure:2QBF , PDB:Structure:2QBH , PDB:Structure:2QBJ , PDB:Structure:2QOU , PDB:Structure:2QOW , PDB:Structure:2QOY , PDB:Structure:2QP0 , PDB:Structure:2VHO , PDB:Structure:2VHP , PDB:Structure:2WWL , PDB:Structure:2YKR , PDB:Structure:2Z4K , PDB:Structure:2Z4M , PDB:Structure:3DF1 , PDB:Structure:3DF3 , PDB:Structure:3E1A , PDB:Structure:3E1C , PDB:Structure:3FIH , PDB:Structure:3I1M , PDB:Structure:3I1O , PDB:Structure:3I1Q , PDB:Structure:3I1S , PDB:Structure:3I1Z , PDB:Structure:3I21 , PDB:Structure:3IZV , PDB:Structure:3IZW , PDB:Structure:3J00 , PDB:Structure:3J0U , PDB:Structure:3J0V , PDB:Structure:3J0X , PDB:Structure:3J0Z , PDB:Structure:3J10 , PDB:Structure:3J13 , PDB:Structure:3J18 , PDB:Structure:3J36 , PDB:Structure:3KC4 , PDB:Structure:3OAQ , PDB:Structure:3OAR , PDB:Structure:3OFA , PDB:Structure:3OFB , PDB:Structure:3OFO , PDB:Structure:3OFP , PDB:Structure:3OFX , PDB:Structure:3OFY , PDB:Structure:3OR9 , PDB:Structure:3ORA , PDB:Structure:3SFS , PDB:Structure:3UOQ , PDB:Structure:4A2I , PDB:Structure:4ADV , PDB:Structure:4GAQ , PDB:Structure:4GAS , PDB:Structure:4GD1 , PDB:Structure:4GD2 , PDB:Structure:4KIY , PDB:Structure:4KJ0 , PDB:Structure:4KJ2 , PDB:Structure:4KJ4 , PDB:Structure:4KJ6 , PDB:Structure:4KJ8 , PDB:Structure:4KJA , PDB:Structure:4KJC , Pfam:IN-FAMILY:PF01084 , Prints:IN-FAMILY:PR00974 , ProDom:IN-FAMILY:PD002239 , Prosite:IN-FAMILY:PS00057

Summary:
The S18 protein is a component of the 30S subunit of the ribosome.

The N-terminal alanine residue of S18 is acetylated by the RimI enzyme [Isono80, Arnold99]. N-terminal acetylation of S18 and S5 correlates with correct folding of the platform and central pseudoknot domains of 16S rRNA [Clatterbuck13].

S18 interacts with the central domain of 16S rRNA; the interaction is dependent on S8 and S15 [Gregory84, Moine88, Stern88]. S18 may be involved in binding of aminoacyl-tRNA to the P site of the ribosome [Ginzburg73]. S18 is photoaffinity labeled by puromycin, an analog of the 3' end of aminoacylated tRNA [Bischof94].

S18 was also shown to crosslink to IF3 [MacKeen80, Cooperman81], IF1 [Boileau83] and 4.5S RNA [Gu05].

Expression analysis of rpsFp indicates that it may be autoregulated by one or more of its operon components [Nakayashiki13]. Coexpressed S6:S18 were found to bind to the rpsF 5'-UTR in a region with structural similarity to their binding site in 16S rRNA. S6 together with S18 may thus be responsible for autoregulation of the rpsF-priB-rpsR-rplI operon [Matelska13].

Review: [Nesterchuk11]

Essentiality data for rpsR knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 30S ribosomal subunit: 30S ribosomal subunit protein S19

Synonyms: RpsS

Gene: rpsS Accession Numbers: EG10918 (EcoCyc), b3316, ECK3303

Locations: cytosol, ribosome

Sequence Length: 92 AAs

Molecular Weight: 10.43 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0000049 - tRNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022627 - cytosolic small ribosomal subunit Inferred from experiment [Hindennach71, WittmannLiebold73]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0015935 - small ribosomal subunit Inferred by computational analysis [GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-47904N , DisProt:DP00147 , EcoliWiki:b3316 , PR:PRO_000023872 , Pride:P0A7U3 , Protein Model Portal:P0A7U3 , RefSeq:NP_417775 , SMR:P0A7U3 , String:511145.b3316 , UniProt:P0A7U3

Relationship Links: InterPro:IN-FAMILY:IPR002222 , InterPro:IN-FAMILY:IPR005732 , InterPro:IN-FAMILY:IPR020934 , InterPro:IN-FAMILY:IPR023575 , Panther:IN-FAMILY:PTHR11880 , PDB:Structure:1M5G , PDB:Structure:1P6G , PDB:Structure:1P87 , PDB:Structure:1VS5 , PDB:Structure:1VS7 , PDB:Structure:2AVY , PDB:Structure:2AW7 , PDB:Structure:2GY9 , PDB:Structure:2GYB , PDB:Structure:2I2P , PDB:Structure:2I2U , PDB:Structure:2QAL , PDB:Structure:2QAN , PDB:Structure:2QB9 , PDB:Structure:2QBB , PDB:Structure:2QBD , PDB:Structure:2QBF , PDB:Structure:2QBH , PDB:Structure:2QBJ , PDB:Structure:2QOU , PDB:Structure:2QOW , PDB:Structure:2QOY , PDB:Structure:2QP0 , PDB:Structure:2VHO , PDB:Structure:2VHP , PDB:Structure:2WWL , PDB:Structure:2YKR , PDB:Structure:2Z4K , PDB:Structure:2Z4M , PDB:Structure:3DF1 , PDB:Structure:3DF3 , PDB:Structure:3E1A , PDB:Structure:3E1C , PDB:Structure:3FIH , PDB:Structure:3I1M , PDB:Structure:3I1O , PDB:Structure:3I1Q , PDB:Structure:3I1S , PDB:Structure:3I1Z , PDB:Structure:3I21 , PDB:Structure:3IZV , PDB:Structure:3IZW , PDB:Structure:3J00 , PDB:Structure:3J0U , PDB:Structure:3J0V , PDB:Structure:3J0X , PDB:Structure:3J0Z , PDB:Structure:3J10 , PDB:Structure:3J13 , PDB:Structure:3J18 , PDB:Structure:3J36 , PDB:Structure:3KC4 , PDB:Structure:3OAQ , PDB:Structure:3OAR , PDB:Structure:3OFA , PDB:Structure:3OFB , PDB:Structure:3OFO , PDB:Structure:3OFP , PDB:Structure:3OFX , PDB:Structure:3OFY , PDB:Structure:3OR9 , PDB:Structure:3ORA , PDB:Structure:3SFS , PDB:Structure:3UOQ , PDB:Structure:4A2I , PDB:Structure:4ADV , PDB:Structure:4GAQ , PDB:Structure:4GAS , PDB:Structure:4GD1 , PDB:Structure:4GD2 , PDB:Structure:4KIY , PDB:Structure:4KJ0 , PDB:Structure:4KJ2 , PDB:Structure:4KJ4 , PDB:Structure:4KJ6 , PDB:Structure:4KJ8 , PDB:Structure:4KJA , PDB:Structure:4KJC , Pfam:IN-FAMILY:PF00203 , Prints:IN-FAMILY:PR00975 , Prosite:IN-FAMILY:PS00323

Summary:
The S19 protein is a component of the 30S subunit of the ribosome.

S19 interacts with 16S rRNA [Wiener87, Wiener88]. S13 forms a complex with S19 in order to bind to 16S rRNA at its specific site [Dijk77, Schwarzbauer85, Pohl88]. Binding of S19 to 16S rRNA is necessary and sufficient for converting 16S rRNA into a substrate for m2G966 methyltransferase, while it abolishes activity of m5C967 methyltransferase [Weitzmann91].

S19 can be crosslinked to aminoacyl-tRNA at the ribosomal A site [Lin84, Osswald95] and P site [Rosen93]. S19 was also shown to crosslink to IF3 [Boileau83].

The ribosome maturation protein RimM binds to S19 in the 30S subunit. An rpsS mutation suppresses the polysome and 16S rRNA processing deficiencies of a rimM point mutant, but not a rimM deletion mutant [Lovgren04].

Essentiality data for rpsS knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 30S ribosomal subunit: 30S ribosomal subunit protein S20

Synonyms: SupS, RpsT

Gene: rpsT Accession Numbers: EG10919 (EcoCyc), b0023, ECK0024

Locations: cytosol, ribosome

Sequence Length: 87 AAs

Molecular Weight: 9.684 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0043086 - negative regulation of catalytic activity Inferred from experiment [Panagiotidis84]
GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0008073 - ornithine decarboxylase inhibitor activity Inferred from experiment [Panagiotidis84]
GO:0070181 - small ribosomal subunit rRNA binding Inferred from experiment [Marquardt79]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022627 - cytosolic small ribosomal subunit Inferred from experiment [Hindennach71, WittmannLiebold73]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation
regulation type of regulation posttranscriptional inhibition / activation of enzymes

Unification Links: DIP:DIP-35857N , EcoliWiki:b0023 , PR:PRO_000023873 , Pride:P0A7U7 , Protein Model Portal:P0A7U7 , RefSeq:NP_414564 , SMR:P0A7U7 , String:511145.b0023 , UniProt:P0A7U7

Relationship Links: InterPro:IN-FAMILY:IPR002583 , PDB:Structure:1M5G , PDB:Structure:1P6G , PDB:Structure:1P87 , PDB:Structure:1VS5 , PDB:Structure:1VS7 , PDB:Structure:2AVY , PDB:Structure:2AW7 , PDB:Structure:2GY9 , PDB:Structure:2GYB , PDB:Structure:2I2P , PDB:Structure:2I2U , PDB:Structure:2QAL , PDB:Structure:2QAN , PDB:Structure:2QB9 , PDB:Structure:2QBB , PDB:Structure:2QBD , PDB:Structure:2QBF , PDB:Structure:2QBH , PDB:Structure:2QBJ , PDB:Structure:2QOU , PDB:Structure:2QOW , PDB:Structure:2QOY , PDB:Structure:2QP0 , PDB:Structure:2VHP , PDB:Structure:2WWL , PDB:Structure:2YKR , PDB:Structure:2Z4K , PDB:Structure:2Z4M , PDB:Structure:3DF1 , PDB:Structure:3DF3 , PDB:Structure:3E1A , PDB:Structure:3E1C , PDB:Structure:3FIH , PDB:Structure:3I1M , PDB:Structure:3I1O , PDB:Structure:3I1Q , PDB:Structure:3I1S , PDB:Structure:3I1Z , PDB:Structure:3I21 , PDB:Structure:3IZV , PDB:Structure:3IZW , PDB:Structure:3J00 , PDB:Structure:3J0U , PDB:Structure:3J0V , PDB:Structure:3J0X , PDB:Structure:3J0Z , PDB:Structure:3J10 , PDB:Structure:3J13 , PDB:Structure:3J18 , PDB:Structure:3J36 , PDB:Structure:3KC4 , PDB:Structure:3OAQ , PDB:Structure:3OAR , PDB:Structure:3OFA , PDB:Structure:3OFB , PDB:Structure:3OFO , PDB:Structure:3OFP , PDB:Structure:3OFX , PDB:Structure:3OFY , PDB:Structure:3OR9 , PDB:Structure:3ORA , PDB:Structure:3SFS , PDB:Structure:3UOQ , PDB:Structure:4A2I , PDB:Structure:4ADV , PDB:Structure:4GAQ , PDB:Structure:4GAS , PDB:Structure:4GD1 , PDB:Structure:4GD2 , PDB:Structure:4KIY , PDB:Structure:4KJ0 , PDB:Structure:4KJ2 , PDB:Structure:4KJ4 , PDB:Structure:4KJ6 , PDB:Structure:4KJ8 , PDB:Structure:4KJA , PDB:Structure:4KJC , Pfam:IN-FAMILY:PF01649 , ProDom:IN-FAMILY:PD004231

Summary:
The S20 protein is a component of the 30S subunit of the ribosome and appears to be involved in translation initiation and the association of the 30S and 50S subunits [Gotz90]. S20 was also identified as antizyme 1, an inhibitor of the biosynthetic ornithine and arginine decarboxylases; these enzymes are involved in the biosynthesis of polyamine [Panagiotidis84]. S20 is identical to L26.

The synthesis of S20 is regulated at the post-transcriptional level [Parsons83, Wirth81]; in an in vitro system, S20 represses its own synthesis [Wirth82]. However, S20 doesn't show affinity for its own mRNA [Donly88]. The UUG initiation codon appears to be important for regulation [Parsons88]. Processing and degradation of rpsT mRNA have been studied extensively; see for example [Baker03, Mackie00] and references therein. rpsT mRNA stability and translational efficiency are linked [Parsons88, Rapaport94].

S20 physically interacts with ornithine and arginine decarboxylase, and overexpression of S20 decreases the production of polyamine in vivo [Panagiotidis95]. Levels of S20 increase in response to polyamines; the effect is thought to be due to an increase in the level of transcription of rpsT [Huang90].

S20 binds to the 5' domain and the 3' minor domain of 16S rRNA [Marquardt79, Stern88a, Weitzmann93, Cormack91]. C-terminal residues of S20 are required for binding to 16S rRNA [Donly88]. Hydroxyl radical footprinting provided evidence that S20 is located near the bottom of the 30S subunit [Culver98]. Further footprinting studies provided insight into 30S subunit assembly [Dutca08]. S20 has a local effect on the stability of the folded structure of 16S rRNA [Ramaswamy09].

The sup(S20) mutation in rpsT suppresses defects of an alanyl-tRNA synthetase mutant [Bock74, Buckel76]. A spontaneous mutation in rpsT causes a temperature-sensitive phenotype and increases the ability of the ribosome to misread nonsense stop codons [RydenAulin93]. An rpsT null mutant shows impaired growth, but is viable [Bubunenko07]. A 30S ribosomal subunit lacking S20 shows a reduced rate of mRNA binding and 70S complex formation [Tobin10].

Essentiality data for rpsT knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Indeterminate 37 Aerobic 7   Yes [Baba06, Comment 3]
Low [Bubunenko07]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 4]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 3]

Subunit of 30S ribosomal subunit: 30S ribosomal subunit protein S21

Synonyms: RpsU

Gene: rpsU Accession Numbers: EG10920 (EcoCyc), b3065, ECK3055

Locations: cytosol, ribosome

Sequence Length: 71 AAs

Molecular Weight: 8.5 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA01]
Molecular Function: GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022627 - cytosolic small ribosomal subunit Inferred from experiment [Hindennach71, WittmannLiebold73]
GO:0005622 - intracellular Inferred by computational analysis [GOA01]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-47839N , EcoliWiki:b3065 , Mint:MINT-1281887 , PR:PRO_000023874 , Pride:P68679 , Protein Model Portal:P68679 , RefSeq:NP_417537 , SMR:P68679 , String:511145.b3065 , UniProt:P68679

Relationship Links: InterPro:IN-FAMILY:IPR001911 , InterPro:IN-FAMILY:IPR018278 , PDB:Structure:1VS5 , PDB:Structure:1VS7 , PDB:Structure:2AVY , PDB:Structure:2AW7 , PDB:Structure:2I2P , PDB:Structure:2I2U , PDB:Structure:2QAL , PDB:Structure:2QAN , PDB:Structure:2QB9 , PDB:Structure:2QBB , PDB:Structure:2QBD , PDB:Structure:2QBF , PDB:Structure:2QBH , PDB:Structure:2QBJ , PDB:Structure:2QOU , PDB:Structure:2QOW , PDB:Structure:2QOY , PDB:Structure:2QP0 , PDB:Structure:2VHO , PDB:Structure:2VHP , PDB:Structure:2WWL , PDB:Structure:2YKR , PDB:Structure:2Z4K , PDB:Structure:2Z4M , PDB:Structure:3DF1 , PDB:Structure:3DF3 , PDB:Structure:3E1A , PDB:Structure:3E1C , PDB:Structure:3FIH , PDB:Structure:3I1M , PDB:Structure:3I1O , PDB:Structure:3I1Q , PDB:Structure:3I1S , PDB:Structure:3I1Z , PDB:Structure:3I21 , PDB:Structure:3IZV , PDB:Structure:3IZW , PDB:Structure:3J00 , PDB:Structure:3J0U , PDB:Structure:3J0V , PDB:Structure:3J0X , PDB:Structure:3J0Z , PDB:Structure:3J10 , PDB:Structure:3J13 , PDB:Structure:3J18 , PDB:Structure:3J36 , PDB:Structure:3KC4 , PDB:Structure:3OAQ , PDB:Structure:3OAR , PDB:Structure:3OFA , PDB:Structure:3OFB , PDB:Structure:3OFO , PDB:Structure:3OFP , PDB:Structure:3OFX , PDB:Structure:3OFY , PDB:Structure:3OR9 , PDB:Structure:3ORA , PDB:Structure:3SFS , PDB:Structure:3UOQ , PDB:Structure:4A2I , PDB:Structure:4ADV , PDB:Structure:4GAQ , PDB:Structure:4GAS , PDB:Structure:4GD1 , PDB:Structure:4GD2 , PDB:Structure:4KIY , PDB:Structure:4KJ0 , PDB:Structure:4KJ2 , PDB:Structure:4KJ4 , PDB:Structure:4KJ6 , PDB:Structure:4KJ8 , PDB:Structure:4KJA , PDB:Structure:4KJC , Pfam:IN-FAMILY:PF01165 , Prints:IN-FAMILY:PR00976 , ProDom:IN-FAMILY:PD005521 , Prosite:IN-FAMILY:PS01181

Summary:
The S21 protein is a component of the 30S subunit of the ribosome. S21 was found to associate with the 50S subunit of the ribosome as well as the 30S subunit [Odom84].

Interactions between S21 and 16S rRNA have been mapped [Stern88]. S21 also crosslinks to the 4.5S RNA of the signal recognition particle [Gu05]. Interactions between S21 and mRNA can be shown by fluorescence energy transfer [Czworkowski91] and crosslinking [Brandt92].

S21 is required for full activity of translation initiation [Held74a, Van81]. S21 was also shown to crosslink to IF3 [MacKeen80, Cooperman81].

Processing and degradation of the rpsU-dnaG-rpoD operon mRNA has been studied; see for example [Yajnik93, Lupski84] and references therein.

Review: [Lupski84]

Essentiality data for rpsU knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Yamamoto09]

Subunit of 30S ribosomal subunit: 30S ribosomal subunit protein S22

Synonyms: Sra, RpsV, Protein D

Gene: sra Accession Numbers: EG11508 (EcoCyc), b1480, ECK1474

Locations: cytosol, ribosome

Sequence Length: 45 AAs

Molecular Weight: 5.096 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA01]
Molecular Function: GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005840 - ribosome Inferred by computational analysis [GOA01]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-48175N , EcoliWiki:b1480 , Mint:MINT-1322613 , PR:PRO_000023982 , Pride:P68191 , Protein Model Portal:P68191 , RefSeq:NP_415997 , String:511145.b1480 , UniProt:P68191

Relationship Links: InterPro:IN-FAMILY:IPR012607 , Pfam:IN-FAMILY:PF08136 , ProDom:IN-FAMILY:PD049510

Summary:
Sra is a sub-stoichiometric component of the 30S ribosomal subunit that is more abundant at stationary phase than during log phase growth [Wada86, Izutsu01]. The amino-terminal methionine residue is not cleaved [Arnold99].

Transcription is induced [Selinger00, Izutsu01] and protein abundance increases [Izutsu01] under stationary phase conditions. σS, cAMP, ppGpp, Fis, and Ihf may be involved in the transcription of sra during stationary phase [Izutsu01]. sra is also cotranscribed with the bdm gene from a promoter upstream of bdm which is activated by osmotic shock and dependent on the RcsCDB phosphorelay system [FrancezCharlot05].

An sra deletion mutant does not have an obvious growth defect [Izutsu01].

Sra: "stationary-phase-induced ribosome-associated" [Izutsu01]

Essentiality data for sra knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 3]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 4]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 3]

Subunit of ribosome: 50S ribosomal subunit

Synonyms: ribosome, large subunit

Relationship Links: PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:2AW4 , PDB:Structure:2AWB


Subunit of 50S ribosomal subunit: 23S ribosomal RNA (rrlA)

Synonyms: rrlA

Gene: rrlA Accession Numbers: EG30077 (EcoCyc), b3854, ECK3846

Sequence Length: 2902/3 AAs

MultiFun Terms: cell structure ribosomes
information transfer protein related translation
information transfer RNA related rRNA, stable RNA

Unification Links: EcoliWiki:b3854

Reactions known to consume the compound:

Not in pathways:
23S rRNA[periplasmic space] + H2O[periplasmic space] → 2 a single-stranded RNA[periplasmic space]


rRNA + S-adenosyl-L-methionine → rRNA containing N6,N6-dimethyladenine + S-adenosyl-L-homocysteine


23S rRNA[periplasmic space] + H2O[periplasmic space] → 2 a single-stranded RNA[periplasmic space]

Reactions known to produce the compound:

tRNA processing :
a tRNA precursor with a 5' extension and a short 3' extension + H2O → a tRNA precursor with a short 3' extension + a single-stranded RNA
a tRNA precursor with a 5' extension + H2O → an uncharged tRNA + a single-stranded RNA

Not in pathways:
an mRNA + H2O → a single-stranded RNA + a single-stranded RNA
an mRNA + H2O → a single-stranded RNA + a single-stranded RNA
RNase E degradation substrate mRNA + n H2O → n a single-stranded RNA
YhaV endonuclease degradation substrate rRNA + H2O → 2 a single-stranded RNA
YhaV endonuclease degradation substrate mRNA + H2O → 2 a single-stranded RNA
RNase III mRNA processing substrate + 2 H2O → RNase III processing product mRNA + 2 a single-stranded RNA
an mRNA[periplasmic space] + H2O[periplasmic space] → 2 a single-stranded RNA[periplasmic space]
RNase G degradation substrate mRNA + H2O → 2 a single-stranded RNA
9S rRNA + 2 H2O → 5S rRNA + 2 a single-stranded RNA
RNase E mRNA processing substrate + n H2O → RNase E processing product mRNA + n a single-stranded RNA

Reactions known to both consume and produce the compound:

Not in pathways:
a single-stranded RNA + phosphate ↔ a single-stranded RNA + a nucleoside diphosphate

In Reactions of unknown directionality:

Not in pathways:
rRNA[periplasmic space] = 2 a single-stranded RNA[periplasmic space]


rRNA[periplasmic space] = 2 a single-stranded RNA[periplasmic space]

Summary:
The 23S and 5S rRNAs are the RNA components of the large subunit (50S subunit) of the E. coli ribosome.

There are seven ribosomal RNA (rRNA) operons, called rrnA, rrnB, rrnC, rrnD, rrnE, rrnG, and rrnH. Each operon contains a 16S rRNA gene, a 23S rRNA gene, and a 5S rRNA gene (except the rrnD operon, which contains two 5S rRNA genes) interspersed with various tRNA genes. Regarding nomenclature, "rrs" genes encode 16S rRNAs, "rrl" genes encode 23S rRNAs, and "rrf" genes encode 5S rRNAs [Neidhardt96].

The sequence and structure of the 23S rRNA has been described, and the relationship of the 23S rRNA to ribosome assembly, structure, and function has been characterized. Interactions between the 23S rRNA and ribosomal proteins have been described.

The relationship of the 23S rRNA to sensitivity to multiple antibiotics is discussed. 23S rRNA also encodes a short peptide that plays a role in erythromycin resistance.

Analysis of mutations in 23S rRNA has been conducted.

The 23S rRNA is subject to pseudouridylation, dihydrouridylation, and methylation. Processing and modification of the 23S rRNA has been characterized. Possible roles for the modified nucleotides have been proposed [Sergiev07].

Reviews describing these results are available.

Regulation has been described in detail; for a review see [Schneider03].

Reviews: [Arthur87, BrissonNoel88, Dahlberg89, Srivastava91, Brimacombe91, Brimacombe92, Lane92, Mueller95, Wower95, Tenson95, Liebman95, Douthwalte95, Triman96a, Triman97, Triman98, Triman99, Charette00, Nakajima99, Stark02, Kim01b].


Subunit of 50S ribosomal subunit: 5S ribosomal RNA (rrfA)

Synonyms: rrfA

Gene: rrfA Accession Numbers: EG30070 (EcoCyc), b3855, ECK3847

Sequence Length: 39 AAs

MultiFun Terms: cell structure ribosomes
information transfer protein related translation
information transfer RNA related rRNA, stable RNA

Unification Links: EcoliWiki:b3855

Reactions known to consume the compound:

Not in pathways:
rRNA + S-adenosyl-L-methionine → rRNA containing N6,N6-dimethyladenine + S-adenosyl-L-homocysteine

Reactions known to produce the compound:

Not in pathways:
9S rRNA + 2 H2O → 5S rRNA + 2 a single-stranded RNA

tRNA processing :
a tRNA precursor with a 5' extension and a short 3' extension + H2O → a tRNA precursor with a short 3' extension + a single-stranded RNA
a tRNA precursor with a 5' extension + H2O → an uncharged tRNA + a single-stranded RNA


an mRNA + H2O → a single-stranded RNA + a single-stranded RNA
an mRNA + H2O → a single-stranded RNA + a single-stranded RNA
RNase E degradation substrate mRNA + n H2O → n a single-stranded RNA
YhaV endonuclease degradation substrate rRNA + H2O → 2 a single-stranded RNA
YhaV endonuclease degradation substrate mRNA + H2O → 2 a single-stranded RNA
RNase III mRNA processing substrate + 2 H2O → RNase III processing product mRNA + 2 a single-stranded RNA
23S rRNA[periplasmic space] + H2O[periplasmic space] → 2 a single-stranded RNA[periplasmic space]
an mRNA[periplasmic space] + H2O[periplasmic space] → 2 a single-stranded RNA[periplasmic space]
RNase G degradation substrate mRNA + H2O → 2 a single-stranded RNA
9S rRNA + 2 H2O → 5S rRNA + 2 a single-stranded RNA
RNase E mRNA processing substrate + n H2O → RNase E processing product mRNA + n a single-stranded RNA

Reactions known to both consume and produce the compound:

Not in pathways:
a single-stranded RNA + phosphate ↔ a single-stranded RNA + a nucleoside diphosphate

In Reactions of unknown directionality:

Not in pathways:
rRNA[periplasmic space] = 2 a single-stranded RNA[periplasmic space]


rRNA[periplasmic space] = 2 a single-stranded RNA[periplasmic space]

Summary:
The 5S and 23S rRNAs are the RNA components of the large subunit (50S subunit) of the E. coli ribosome.

There are seven ribosomal RNA (rRNA) operons, called rrnA, rrnB, rrnC, rrnD, rrnE, rrnG, and rrnH. Each operon contains a 16S rRNA gene, a 23S rRNA gene, and a 5S rRNA gene (except the rrnD operon, which contains two 5S rRNA genes) interspersed with various tRNA genes. Regarding nomenclature, "rrs" genes encode 16S rRNAs, "rrl" genes encode 23S rRNAs, and "rrf" genes encode 5S rRNAs [Neidhardt96].

The sequence and structure of the 5S rRNA has been described, and the relationship of the 5S rRNA to ribosome assembly, structure, and function has been characterized. Interactions between the 5S rRNA and 23S rRNA as well as ribosomal proteins have been described. Mutations in 5S rRNA have been analyzed, and the post-transcriptional processing of the 5S rRNA has been characterized.

Reviews describing these results are available.

Regulation has been described in detail; for a review see [Schneider03].

Reviews: [Lind, Azad79, Tanaka85, Nowotny88a, Moore88a, Vester88, Goringer88, Srivastava91, Barciszewska96, Barciszewska97].


Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L1

Synonyms: Rpy, RplA

Gene: rplA Accession Numbers: EG10864 (EcoCyc), b3984, ECK3975

Locations: cytosol, ribosome

Sequence Length: 234 AAs

Molecular Weight: 24.73 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0045947 - negative regulation of translational initiation Inferred from experiment [Baughman83]
GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
GO:0006417 - regulation of translation Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Arifuzzaman06, Butland05]
GO:0000049 - tRNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11]
GO:0015934 - large ribosomal subunit Inferred by computational analysis [GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation
regulation type of regulation posttranscriptional

Unification Links: DIP:DIP-35746N , EcoliWiki:b3984 , Mint:MINT-1268287 , ModBase:P0A7L0 , PR:PRO_000023809 , Pride:P0A7L0 , Protein Model Portal:P0A7L0 , RefSeq:NP_418411 , SMR:P0A7L0 , String:511145.b3984 , Swiss-Model:P0A7L0 , UniProt:P0A7L0

Relationship Links: InterPro:IN-FAMILY:IPR002143 , InterPro:IN-FAMILY:IPR005878 , InterPro:IN-FAMILY:IPR016094 , InterPro:IN-FAMILY:IPR016095 , InterPro:IN-FAMILY:IPR023673 , InterPro:IN-FAMILY:IPR023674 , InterPro:IN-FAMILY:IPR028364 , PDB:Structure:1EG0 , PDB:Structure:1ML5 , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2RDO , PDB:Structure:2WWQ , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:487D , Pfam:IN-FAMILY:PF00687 , Prosite:IN-FAMILY:PS01199

Summary:
The L1 protein is a component of the 50S subunit of the ribosome and also functions in the post-transcriptional regulation of the ribosomal protein genes encoded in the L11 operon. Ribosomes lacking L1 show a lower translation activity than wild type [Subramanian80] and are defective in binding of aminoacylated tRNA [Sander83]. L1 has been identified within a 3-D map of the 70S ribosome constructed by cryo-electron microscopy [Malhotra98].

L1 interacts with a region in the 5' end of 23S rRNA [Branlant76, Branlant80, Egebjerg91]. It also can be crosslinked to a region near the central fold of aminoacylated tRNA in the P and E site [Podkowinski89, Rosen93, Osswald95]. L1 is located within 21 Å of nucleotide C2475 of 23S rRNA, near the peptidyltransferase center [Muralikrishna95].

L1 is a translational repressor of the synthesis of L11 and L1, the proteins encoded by the L11 operon [Brot81, Thomas87, Stoffler81, Yates80, Dabbs81]. Synthesis of L1 is regulated by translational coupling to the synthesis of L11 [Yates81, Baughman83]. The target site for L1 binding to the mRNA is near the translation initiation site of L11 [Yates81, Baughman83, Thomas87a], and the presence of 23S rRNA relieves translational inhibition by L1 [Yates81]. The predicted secondary structure of the L1 binding region within 23S rRNA and rplKA mRNA is similar [Branlant80, Gourse81] and has been studied experimentally [Baughman84, Kearney87, Said88, Drygin00].

Both the growth rate control and stringent control of the synthesis of ribosomal proteins L11 and L1 are resulting from translational regulation by L1 [Cole86].

Essentiality data for rplA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 3]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 4]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 3]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L2

Synonyms: RplB

Gene: rplB Accession Numbers: EG10865 (EcoCyc), b3317, ECK3304

Locations: cytosol, ribosome

Sequence Length: 273 AAs

Molecular Weight: 29.86 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Chodavarapu11, Rippa10, Arifuzzaman06, Butland05]
GO:0008270 - zinc ion binding Inferred from experiment [Katayama02]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0016740 - transferase activity Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment [Ishihama08, Zhang07]
GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a]
GO:0005622 - intracellular Inferred by computational analysis [GOA01]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0015934 - large ribosomal subunit Inferred by computational analysis [GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-35747N , EcoliWiki:b3317 , Mint:MINT-1322809 , ModBase:P60422 , PR:PRO_000023810 , Pride:P60422 , Protein Model Portal:P60422 , RefSeq:NP_417776 , SMR:P60422 , String:511145.b3317 , UniProt:P60422

Relationship Links: InterPro:IN-FAMILY:IPR002171 , InterPro:IN-FAMILY:IPR005880 , InterPro:IN-FAMILY:IPR008991 , InterPro:IN-FAMILY:IPR012340 , InterPro:IN-FAMILY:IPR014722 , InterPro:IN-FAMILY:IPR014726 , InterPro:IN-FAMILY:IPR022666 , InterPro:IN-FAMILY:IPR022669 , InterPro:IN-FAMILY:IPR022671 , Panther:IN-FAMILY:PTHR13691 , Panther:IN-FAMILY:PTHR13691:SF5 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2VHM , PDB:Structure:2VHN , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3DF2 , PDB:Structure:3DF4 , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:487D , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF00181 , Pfam:IN-FAMILY:PF03947 , Prosite:IN-FAMILY:PS00467

Summary:
The L2 protein is a component of the 50S subunit of the ribosome and is part of the peptidyltransferase center. L2 is highly evolutionarily conserved [Schmid84, Uhlein98].

L2 is required for the association of the 30S and 50S subunits [Diedrich00]; one end of the elongated L2 protein is located at the intersubunit interface of the 50S subunit [Willumeit01]. L2 is involved in binding of tRNA to both the A and P sites, and the His229 residue appears to be important for peptidyl-transferase activity of the ribosome [Diedrich00]. A conserved region within L2 is required for assembly of L16 into the 50S ribosomal subunit [Romero90]. Ribosome modulation factor binds near L2, L13, and S13 [Yoshida02].

L2 interacts with domains II and IV of 23S rRNA [Egebjerg91, Beauclerk88, Thiede98, Ostergaard98] and with 5S rRNA [Okada00]. L2 also interacts with aminoacyl-tRNA [Metspalu81, Remme85, Sumpter90].

Essentiality data for rplB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L3

Synonyms: RplC

Gene: rplC Accession Numbers: EG10866 (EcoCyc), b3320, ECK3307

Locations: cytosol, ribosome

Sequence Length: 209 AAs

Molecular Weight: 22.243 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Zheng11]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: EcoliWiki:b3320 , Mint:MINT-1302843 , ModBase:P60438 , PR:PRO_000023811 , Pride:P60438 , Protein Model Portal:P60438 , RefSeq:NP_417779 , SMR:P60438 , String:511145.b3320 , UniProt:P60438

Relationship Links: InterPro:IN-FAMILY:IPR000597 , InterPro:IN-FAMILY:IPR009000 , InterPro:IN-FAMILY:IPR019926 , InterPro:IN-FAMILY:IPR019927 , Panther:IN-FAMILY:PTHR11229 , PDB:Structure:1ML5 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2VHM , PDB:Structure:2VHN , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3DF2 , PDB:Structure:3DF4 , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF00297 , Prosite:IN-FAMILY:PS00474

Summary:
The L3 protein is a component of the 50S subunit of the ribosome. L3 and L24 are the two proteins that initiate assembly of the 50S subunit [Nowotny82].

The L3 protein is methylated at the glutamine residue in position 150 [Lhoest77, Arnold99]. A prmB mutant which lacks methylation of L3 has a cold-sensitive growth phenotype and accumulates abnormal ribosomal particles; however, lack of L3 methylation does not appear to affect ribosome function once the ribosome is assembled [Lhoest81].

L3 interacts with 23S rRNA [Uchiumi99]; this interaction appears to be cooperative with L6 [Uchiumi99].

An L3 mutant strain is resistant to the antibiotics tiamulin (a peptidyl transferase inhibitor) and pleuromutilin, but not valnemulin [Bosling03, Long06]. An amber mutation in rplC exerts a polar effect on the genes distal to the rplC gene in the S10 operon [Cabezon80].

Essentiality data for rplC knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L4

Synonyms: EryA, RplD

Gene: rplD Accession Numbers: EG10867 (EcoCyc), b3319, ECK3306

Locations: cytosol, ribosome

Sequence Length: 201 AAs

Molecular Weight: 22.086 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0017148 - negative regulation of translation Inferred from experiment [Yates80a]
GO:0060702 - negative regulation of endoribonuclease activity Inferred from experiment [Singh09]
GO:0006351 - transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0006353 - DNA-templated transcription, termination Inferred by computational analysis [UniProtGOA11]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11]
GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
GO:0006417 - regulation of translation Inferred by computational analysis [UniProtGOA11]
GO:0046677 - response to antibiotic Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Singh09]
GO:0030371 - translation repressor activity Inferred from experiment [Yates80a]
GO:0060698 - endoribonuclease inhibitor activity Inferred from experiment [Singh09]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Zhang07]
GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation
regulation genetic unit regulated operon
regulation type of regulation posttranscriptional translation attenuation and efficiency
regulation type of regulation transcriptional level

Unification Links: DIP:DIP-35791N , DisProt:DP00600 , EcoliWiki:b3319 , Mint:MINT-1219709 , ModBase:P60723 , PR:PRO_000023812 , Pride:P60723 , Protein Model Portal:P60723 , RefSeq:NP_417778 , SMR:P60723 , String:511145.b3319 , UniProt:P60723

Relationship Links: InterPro:IN-FAMILY:IPR002136 , InterPro:IN-FAMILY:IPR013005 , InterPro:IN-FAMILY:IPR023574 , Panther:IN-FAMILY:PTHR10746 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2VHM , PDB:Structure:2VHN , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3DF2 , PDB:Structure:3DF4 , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF00573

Summary:
The L4 protein is a component of the 50S subunit of the ribosome and also regulates the expression of S10 operon at both the transcriptional and posttranscriptional level. The functions of L4 in ribosome assembly, attenuation, and translational regulation of the operon are separable [Freedman87, Li96a].

Addition of L4 to an in vitro protein synthesis reaction inhibits the synthesis of the promoter-proximal proteins in the S10 operon, suggesting that L4 may be an inhibitor of translation [Yates80a]. In vivo, overproduction of L4 was found to reduce the synthesis of S10 operon mRNA [Zengel80]. The steady-state growth rate-dependent control of the S10 operon expression requires additional factors [Lindahl90].

L4 stimulates premature termination (transcription attenuation) at a NusA-dependent terminator site 30 bases upstream of the first structural gene of the S10 operon, and termination requires the function of NusA [Lindahl83, Zengel90]. The attenuator hairpin region is sufficient for NusA-dependent pausing, and a second hairpin region immediately upstream of the attenuator hairpin is necessary for L4 to prolong the pause [Zengel92, Sha95, Zengel96]. Structural and sequence requirements for L4-mediated transcription termination within the S10 leader region have been determined [Zengel02]; the first 150 bases of the S10 leader region are sufficient for L4-mediated attenuation control [Zengel90a], and a 64-nucleotide sequence is required for L4 interaction with the S10 leader mRNA [Stelzl03]. Binding of L4 to the leader region induces structural changes in the mRNA [Stelzl03]. A region of 110 bases within domain I of 23S rRNA competes with paused transcription complex for binding of L4 [Zengel91, Zengel93].

L4 interacts with the 5' segment of 23S rRNA [Spierer75, Gulle88, Maly80, Urlaub95, Thiede98]. The L4 and L24 binding sites in 23S rRNA localize to a small fragment [Stelzl00] and may be a key element for rRNA folding in the early assembly pathway for the ribosome [Stelzl01]. The L4 binding region within domain I of 23S rRNA has three-dimensional structural similarity to its binding region on the S10 operon leader mRNA where it inhibits its own translation [Ostergaard98, Stelzl03].

L4 is a component of the binding site for erythromycin on the ribosome [Arevalo88]. An L4 K63E mutant is resistant to erythromycin, has a cold-sensitive growth defect, and shows a defect in 50S subunit assembly [Apirion67, Wittmann73, Chittum94]. The mutation reduces the rate of erythromycin association as well as equilibrium binding [Lovmar09]. Additional L4 mutants that confer erythromycin resistance have been isolated; all map to the extended loop region of L4 [Zaman07]. A large number of additional alleles was isolated by recombineering [Diner09]. L4, L5, and L21 bind to erythromycin cooperatively [Pye90]. The extended loop region of L4 (amino acids 40-88) contributes to the lining of the peptide exit tunnel in the ribosome and is contacted by the growing peptide chain [Houben05]. While deletions of this region of L4 do not appear to affect function of L4 [Zengel03], the K63E point mutation that results in erythromycin resistance alters the decoding accuracy of the ribosome [OConnor04]. Various mutations in L4 affect peptide-induced pausing of translation [Lawrence08].

L4 directly interacts with the C-terminal domain of RNase E and inhibits its activity. A number of mRNAs are stabilized by ectopic expression of L4 [Singh09].

Citations: [Gagnon10, Dunkle10, Kostopoulou12, Fu13]

Essentiality data for rplD knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L5

Synonyms: RplE

Gene: rplE Accession Numbers: EG10868 (EcoCyc), b3308, ECK3295

Locations: cytosol, ribosome

Sequence Length: 179 AAs

Molecular Weight: 20.302 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0000049 - tRNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Zhang07]
GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a]
GO:0005622 - intracellular Inferred by computational analysis [GOA01]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-35914N , EcoliWiki:b3308 , Mint:MINT-1238892 , PR:PRO_000023813 , Pride:P62399 , Protein Model Portal:P62399 , RefSeq:NP_417767 , SMR:P62399 , String:511145.b3308 , UniProt:P62399

Relationship Links: InterPro:IN-FAMILY:IPR002132 , InterPro:IN-FAMILY:IPR020929 , InterPro:IN-FAMILY:IPR020930 , InterPro:IN-FAMILY:IPR022803 , Panther:IN-FAMILY:PTHR11994 , PDB:Structure:1ML5 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2VHM , PDB:Structure:2VHN , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3DF2 , PDB:Structure:3DF4 , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF00281 , Pfam:IN-FAMILY:PF00673 , Prosite:IN-FAMILY:PS00358

Summary:
The L5 protein is a component of the 50S subunit of the ribosome. The crystal structure of the ribosome [Schuwirth05], cryo-EM reconstructions [Gao03a], and crosslinking experiments [Lambert81] show that the L5 protein contacts the S13 protein of the small subunit of the ribosome.

L5 binds to 5S rRNA [Huber84, Shpanchenko96]. The association of L5 with 5S rRNA is cooperatively stimulated by L18 [Spierer78], and the binding regions of the 5S rRNA-L5-L18 complex were mapped [Ostergaard98]. L5 also crosslinks to aminoacylated tRNA in the P site of the ribosome [Osswald95].

L4, L5, and L21 bind to erythromycin cooperatively [Pye90]. L5 is altered in a thiopeptin-resistant mutant [Liou75].

Essentiality data for rplE knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L6

Synonyms: RplF

Gene: rplF Accession Numbers: EG10869 (EcoCyc), b3305, ECK3292

Locations: cytosol, ribosome

Sequence Length: 177 AAs

Molecular Weight: 18.904 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
GO:0046677 - response to antibiotic Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11, GOA06, GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a]
GO:0005622 - intracellular Inferred by computational analysis [GOA01]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-35860N , EcoliWiki:b3305 , Mint:MINT-1244940 , PR:PRO_000023814 , Pride:P0AG55 , Protein Model Portal:P0AG55 , RefSeq:NP_417764 , SMR:P0AG55 , String:511145.b3305 , Swiss-Model:P0AG55 , UniProt:P0AG55

Relationship Links: InterPro:IN-FAMILY:IPR000702 , InterPro:IN-FAMILY:IPR002358 , InterPro:IN-FAMILY:IPR019906 , InterPro:IN-FAMILY:IPR020040 , Panther:IN-FAMILY:PTHR11655 , Panther:IN-FAMILY:PTHR11655:SF6 , PDB:Structure:1EG0 , PDB:Structure:1ML5 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2VHM , PDB:Structure:2VHN , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:487D , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF00347 , Prints:IN-FAMILY:PR00059 , Prosite:IN-FAMILY:PS00525

Summary:
The L6 protein is a component of the 50S subunit of the ribosome.

L6 interacts with 23S rRNA [Urlaub95, Osswald90, Uchiumi99]. Interaction appears to be cooperative with L3 [Uchiumi99]. L6 crosslinks to the stem-loop structure in domain V of 23S rRNA [Wower81], but assembles to domain VI [Leffers88]. The L6 binding site within domain VI has been identified [Stelzl00].

L6 is altered in a gentamicin-resistant mutant [Buckel77]. Ribosomes of gentamicin-resistant L6 mutants have altered misreading properties; the L6 alteration is thought to change a parameter of the ribosome function involved in codon recognition [Kuhberger79]. L6 also participates in the binding of dibekacin to ribosomes [Akiyama81].

Mutations in L6 cause a cold-sensitive growth defect as well as defective assembly and maturation of the 30S and 50S subunits of the ribosome at low temperature [Bosl81].

Essentiality data for rplF knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 50S ribosomal subunit: 50S ribosomal protein complex L8

Summary:
The ribosomal proteins L10 and L7/L12 form a complex of two L7/L12 dimers and one L10 monomer; the complex can be isolated both in solution and from intact ribosomes and was previously identified as L8 [Pettersson76, Chu76, Osterberg77, Gudkov78]. The conformation of the L8 complex and changes in L7/L12 dimer conformation upon binding to the ribosome or L10 has been studied [Makarov93, Hamman96, Bocharov98].

The binding site within 23S rRNA of the L8 complex has been determined [Beauclerk84, Rosendahl93].


Subunit of 50S ribosomal protein complex L8: 50S ribosomal subunit protein L10

Synonyms: RplJ

Gene: rplJ Accession Numbers: EG10871 (EcoCyc), b3985, ECK3976

Locations: cytosol, ribosome

Sequence Length: 165 AAs

Molecular Weight: 17.712 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
GO:0006417 - regulation of translation Inferred by computational analysis [UniProtGOA11]
GO:0042254 - ribosome biogenesis Inferred by computational analysis [GOA01]
Molecular Function: GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11]
GO:0070180 - large ribosomal subunit rRNA binding Inferred by computational analysis [GOA06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Zhang07, LopezCampistrou05]
GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a]
GO:0005622 - intracellular Inferred by computational analysis [GOA01]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation
regulation type of regulation posttranscriptional translation attenuation and efficiency

Unification Links: DIP:DIP-35816N , EcoliWiki:b3985 , Mint:MINT-1264502 , PR:PRO_000023816 , Pride:P0A7J3 , Protein Model Portal:P0A7J3 , RefSeq:NP_418412 , SMR:P0A7J3 , String:511145.b3985 , UniProt:P0A7J3

Relationship Links: InterPro:IN-FAMILY:IPR001790 , InterPro:IN-FAMILY:IPR002363 , InterPro:IN-FAMILY:IPR022973 , Panther:IN-FAMILY:PTHR11560:SF8 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J37 , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ5 , PDB:Structure:4KJ9 , Pfam:IN-FAMILY:PF00466 , Prosite:IN-FAMILY:PS01109

Summary:
The L10 protein is a component of the 50S subunit of the ribosome and also regulates the expression of the L10 (β) operon at the posttranscriptional level.

L10 forms a complex with L7/L12; this complex was originally identified as the L8 subunit [Pettersson76, Chu76, Osterberg77, Gudkov78]. L10 and L7/L12 bind to the 23S rRNA early during assembly of the 50S subunit [deNarvaez79]. Binding of L10 to 23S rRNA can be separated from binding to L7/L12 [Pettersson79]; two binding sites in the C terminus of L10 are required for the binding of two L7/L12 dimers, but not for assembly of L10 into the ribosome [Griaznova00].

Synthesis of L10 and L7/L12 is regulated at the level of translation initiation [Little81, Robakis81]. Expression of L12 is closely linked to expression of L10 [Hui82], and a region within the leader sequence of the L10 operon mRNA regulates the translation efficiency of L10 and L7/L12 [Hui82, Fiil80]. The L10 protein acts at a single site in the leader mRNA [Yates81a]. It has been shown that the region within the leader sequence that is essential for both translational feedback regulation and efficient translation lies between 70 and195 bases upstream of the rplJ translation start [Friesen83], and that secondary structure within that region is required for feedback regulation [Christensen84, Climie87, Climie88]. A complex containing L10 and L12 can bind directly to the leader sequence of the L10 operon mRNA and prevent translation [Johnsen82, Christensen84, Climie88], and added 23S rRNA prevents binding of L10/L12 to the mRNA [Johnsen82]. There is sequence similarity between 23S rRNA and the L10 leader region, and the L10/L12 binding site includes part of the homologous sequences [Johnsen82].

The abundance of L10 is also regulated at the post-translational level. L10 alone is subject to rapid proteolytic decay (half life of 1.5 minutes), but is stable if it is in a complex with L7/L12 [Petersen90].

Essentiality data for rplJ knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 50S ribosomal protein complex L8: 50S ribosomal subunit protein L7/L12 dimer

Gene: rplL Accession Numbers: EG10873 (EcoCyc), b3986, ECK3977

Locations: cytosol, ribosome

Subunit composition of 50S ribosomal subunit protein L7/L12 dimer = [RplL]2
         50S ribosomal subunit protein L12 = RplL

Map Position: [4,178,583 -> 4,178,948] (90.06 centisomes)
Length: 366 bp / 121 aa

Molecular Weight of Polypeptide: 12.295 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a, WittmannLiebold73]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-36009N , EcoliWiki:b3986 , Mint:MINT-1277405 , PR:PRO_000023818 , Pride:P0A7K2 , Protein Model Portal:P0A7K2 , RefSeq:NP_418413 , SMR:P0A7K2 , String:511145.b3986 , UniProt:P0A7K2

Relationship Links: InterPro:IN-FAMILY:IPR000206 , InterPro:IN-FAMILY:IPR008932 , InterPro:IN-FAMILY:IPR013823 , InterPro:IN-FAMILY:IPR014719 , PDB:Structure:1CTF , PDB:Structure:1RQS , PDB:Structure:1RQT , PDB:Structure:1RQU , PDB:Structure:1RQV , PDB:Structure:2BCW , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2XTG , PDB:Structure:2XUX , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:4KIX , Pfam:IN-FAMILY:PF00542 , ProDom:IN-FAMILY:PD001326

Reactions known to consume the compound:

Not in pathways:
50S ribosomal subunit protein L12 + acetyl-CoA → 50S ribosomal subunit protein L7 + coenzyme A

Gene Citations: [Ralling84, Steward91, Barry80]

Essentiality data for rplL knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L9

Synonyms: RplI

Gene: rplI Accession Numbers: EG10870 (EcoCyc), b4203, ECK4199

Locations: cytosol, ribosome

Sequence Length: 149 AAs

Molecular Weight: 15.769 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-35748N , EcoliWiki:b4203 , Mint:MINT-1228834 , ModBase:P0A7R1 , PR:PRO_000023815 , Pride:P0A7R1 , Protein Model Portal:P0A7R1 , RefSeq:NP_418624 , SMR:P0A7R1 , String:511145.b4203 , UniProt:P0A7R1

Relationship Links: InterPro:IN-FAMILY:IPR000244 , InterPro:IN-FAMILY:IPR009027 , InterPro:IN-FAMILY:IPR020069 , InterPro:IN-FAMILY:IPR020070 , InterPro:IN-FAMILY:IPR020594 , Panther:IN-FAMILY:PTHR21368 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2VHM , PDB:Structure:2VHN , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3DF2 , PDB:Structure:3DF4 , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:487D , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF01281 , Pfam:IN-FAMILY:PF03948 , Prosite:IN-FAMILY:PS00651

Summary:
The L9 protein is a component of the 50S subunit of the ribosome.

A solution structure determined by cryo-EM showed that the L9 protein consists of N-terminal and C-terminal domains connected by a long α helical domain that is wrapped around the L1 stalk [Matadeen99].

The binding region of L9 on domain V of 23S rRNA was mapped [Ostergaard98]. The N- and C-terminal domains of L9 interact with two separate sites in domain V of 23S rRNA [Adamski96, Lieberman00]. Crosslinking of tRNA in the A site of the ribosome to L9 depends on the state of the tRNA [Graifer89].

Essentiality data for rplI knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 3]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 4]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 3]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L11

Synonyms: RelC, RplK

Gene: rplK Accession Numbers: EG10872 (EcoCyc), b3983, ECK3974

Locations: cytosol, ribosome

Sequence Length: 142 AAs

Molecular Weight: 14.875 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006415 - translational termination Inferred from experiment [Sato06]
GO:0015968 - stringent response Inferred from experiment [Jenvert07]
GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Arifuzzaman06, Butland05]
GO:0019843 - rRNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, Schmidt81]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0070180 - large ribosomal subunit rRNA binding Inferred by computational analysis [GOA06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment [Ishihama08]
GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a, Dognin80]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-35882N , EcoliWiki:b3983 , Mint:MINT-1232893 , ModBase:P0A7J7 , PR:PRO_000023817 , Pride:P0A7J7 , Protein Model Portal:P0A7J7 , RefSeq:NP_418410 , SMR:P0A7J7 , String:511145.b3983 , UniProt:P0A7J7

Relationship Links: InterPro:IN-FAMILY:IPR000911 , InterPro:IN-FAMILY:IPR006519 , InterPro:IN-FAMILY:IPR020783 , InterPro:IN-FAMILY:IPR020784 , InterPro:IN-FAMILY:IPR020785 , Panther:IN-FAMILY:PTHR11661 , PDB:Structure:1EG0 , PDB:Structure:1MJ1 , PDB:Structure:1ML5 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2VHM , PDB:Structure:2VHN , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3DEG , PDB:Structure:3DF2 , PDB:Structure:3DF4 , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3EP2 , PDB:Structure:3EQ3 , PDB:Structure:3EQ4 , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0D , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:487D , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF00298 , Pfam:IN-FAMILY:PF03946 , Prosite:IN-FAMILY:PS00359 , Smart:IN-FAMILY:SM00649

Reactions known to consume the compound:

Not in pathways:
a non-methylated ribosomal protein L11 + S-adenosyl-L-methionine → a methylated ribosomal protein L11 + S-adenosyl-L-homocysteine

Summary:
The L11 protein is a component of the 50S subunit of the ribosome.

L11 is posttranslationally modified by methylation [Chang75]. The N-terminal alanine residue is methylated to N-trimethylalanine [Lederer77, Dognin80a], and two lysine residues are methylated to Nε, Nε, Nε-trimethyllysine [Dognin80, Jerez80, Dognin80a, Arnold99]. Methylation of L11 does not appear to be essential for its function [Vanet94].

Ribosome core particles lacking L11 do not display EF-G-dependent GTPase activity [Schrier75]. L11 participates in joining the 30S initiation complex to the 50S subunit [Naaktgeboren76, Gotz89]. The N-terminal domain of L11 participates in the formation of the arc-like connection between EF-G and L7/L12 during tRNA translocation [Datta05].

L11 directly interacts with 23S rRNA [Littlechild77]. Its binding site has been identified [Schmidt81] and is adjacent to the L8 complex binding site in 23S rRNA [Beauclerk84, Egebjerg90]. Binding of the L8 complex and L11 appears to be cooperative [Rosendahl93, Rosendahl95]. L11 recognizes and stabilizes the three-dimensional structure of its binding site in 23S rRNA [Ryan91, Blyn00, Bowen05, Maeder06]. A crystal structure of L11 bound to a 58 nucleotide fragment of 23S rRNA has been determined; the C-terminal domain of L11 binds RNA tightly, while the N-terminal domain makes only limited contacts with RNA [Wimberly99].

The L11 binding region of 23S rRNA appears to be important for translation termination [Van02]. The N-terminal domain of L11 is critical for modulation of release factor binding [Tate83, McCaughan84, Tate84, Tate86, Van03]. Deletion of the amino terminus reduces the termination efficiency of RF1, but not RF2, thus increasing nonsense suppression at UAG codons, while changes in L11 reduce dissociation of RF2 from ribosome, causing a decrease in nonsense suppression at UGA codons [Bouakaz06]. Strains lacking L11 exhibit UAG stop codon suppression, defective growth, and high-temperature lethality; strains lacking only the N-terminal domain of L11 are only defective in UAG-dependent termination [Van03]. However, later experiments show that L11 affects RF1 and RF2 activity similarly [Sato06].

L11 is required for binding of the thiazole antibiotic thiostrepton to the ribosome [Highland75].

L11 plays a role in regulating the stringent response; an rplK (relC) mutant has a relaxed phenotype [Friesen74, Parker76]. Both a proline-rich helix in the N-terminal domain of L11 and the linker region between the N- and C-terminal domains are required for regulating the activity of (p)ppGpp synthetase I (RelA) [Yang01, Jenvert07], although no direct interaction between the two proteins has been detected [Yang01]. ppGpp synthesis by RelA requires both uncharged tRNA at the A site of the ribosome and the presence of L11 [Wendrich02]. The L11 N-terminal domain alone can activate RelA in the presence of ribosomes and uncharged tRNA [Jenvert07].

Essentiality data for rplK knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Yamamoto09]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L13

Synonyms: RplM

Gene: rplM Accession Numbers: EG10874 (EcoCyc), b3231, ECK3220

Locations: cytosol, ribosome

Sequence Length: 142 AAs

Molecular Weight: 16.019 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0008270 - zinc ion binding Inferred from experiment [Katayama02]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Zhang07]
GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-47837N , EcoliWiki:b3231 , Mint:MINT-1269598 , ModBase:P0AA10 , PR:PRO_000023819 , Pride:P0AA10 , Protein Model Portal:P0AA10 , RefSeq:NP_417698 , SMR:P0AA10 , String:511145.b3231 , UniProt:P0AA10

Relationship Links: InterPro:IN-FAMILY:IPR005822 , InterPro:IN-FAMILY:IPR005823 , InterPro:IN-FAMILY:IPR023563 , InterPro:IN-FAMILY:IPR023564 , Panther:IN-FAMILY:PTHR11545 , PDB:Structure:1ML5 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF00572 , Prosite:IN-FAMILY:PS00783

Summary:
The L13 protein is an early assembly component of the 50S subunit of the ribosome. The RNA helicase SrmB is necessary for the assembly of L13 into the ribosome [Charollais03].

L13 interacts with 23S rRNA [Spierer75, Spierer76, Skold81, Osswald90, Tumminia94] and crosslinks to it in both free ribosomes and the initiation complex [Chistyakov89]. L13 is located within 21 Å of nucleotide C2475 of 23S rRNA, near the peptidyltransferase center [Muralikrishna95]. L13 binds to 5S rRNA [Kargel87] and can be crosslinked to L2 [Barritault75], L3 [Walleczek89], L20 [Barritault75, Redl89, Walleczek89] and L21 [Schonfeld87, Walleczek89a, Walleczek89]. L13 interacts with tRNA in the P site [Graifer89].

Ribosome modulation factor binds near L2, L13, and S13 [Yoshida02]. A puromycin analog [Krassnigg78], a tobramycin analog [Tangy83], and a pactamycin analog [Tejedor85] can be crosslinked to L13.

L13 has RNA chaperone-like activity in an in vitro trans splicing assay [Semrad04] and binds zinc [Katayama02].

Essentiality data for rplM knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L14

Synonyms: RplN

Gene: rplN Accession Numbers: EG10875 (EcoCyc), b3310, ECK3297

Locations: cytosol, ribosome

Sequence Length: 123 AAs

Molecular Weight: 13.541 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Hauser12]
GO:0070180 - large ribosomal subunit rRNA binding Inferred from experiment [Urlaub95]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a, Kaltschmidt70]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0015934 - large ribosomal subunit Inferred by computational analysis [GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-35798N , EcoliWiki:b3310 , Mint:MINT-1304553 , ModBase:P0ADY3 , PR:PRO_000023820 , Pride:P0ADY3 , Protein Model Portal:P0ADY3 , RefSeq:NP_417769 , SMR:P0ADY3 , String:511145.b3310 , Swiss-Model:P0ADY3 , UniProt:P0ADY3

Relationship Links: InterPro:IN-FAMILY:IPR000218 , InterPro:IN-FAMILY:IPR005745 , InterPro:IN-FAMILY:IPR019972 , InterPro:IN-FAMILY:IPR023571 , Panther:IN-FAMILY:PTHR11761 , Panther:IN-FAMILY:PTHR11761:SF3 , PDB:Structure:1ML5 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:487D , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF00238 , Prosite:IN-FAMILY:PS00049

Summary:
The L14 protein is a component of the 50S subunit of the ribosome.

L14 crosslinks to 23S rRNA [Osswald90, Urlaub95]. In the cryo-EM reconstruction of the ribosome, L14 was modelled to be located at the 30S-50S subunit interface, at bridges B5 and B8 [Gao03a]. In all-atom molecular dynamics simulations of the ribosome, a structural gate between helices 71 and 92 of 23S rRNA restricts tRNA motion and together with L14 acts as a steric filter for the cognate tRNA [Caulfield12].

L14 interacts directly with ribosomal silencing factor. Amino acid residues in L14 that are essential for this interaction have been identified by mutagenesis [Hauser12].

Based on amino-terminal sequencing of the purified protein, L14 may be identical to Rep helicase stimulatory protein (RHSP) [Smith89, Yancey91]. RHSP forms aggregates on DNA and interacts with rRNA [Yancey91].

Retroregulation of L14 expression by mRNA processing and decay has been studied in E. coli B/r [Liang99].

Essentiality data for rplN knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L15

Synonyms: RplO

Gene: rplO Accession Numbers: EG10876 (EcoCyc), b3301, ECK3288

Locations: ribosome

Sequence Length: 144 AAs

Molecular Weight: 14.98 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Butland05]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
Cellular Component: GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0015934 - large ribosomal subunit Inferred by computational analysis [GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-10752N , EcoliWiki:b3301 , Mint:MINT-1260355 , ModBase:P02413 , PR:PRO_000023821 , Pride:P02413 , Protein Model Portal:P02413 , RefSeq:NP_417760 , SMR:P02413 , String:511145.b3301 , UniProt:P02413

Relationship Links: InterPro:IN-FAMILY:IPR001196 , InterPro:IN-FAMILY:IPR005749 , InterPro:IN-FAMILY:IPR021131 , Panther:IN-FAMILY:PTHR12934 , PDB:Structure:1ML5 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2VHM , PDB:Structure:2VHN , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3DF2 , PDB:Structure:3DF4 , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IY9 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF00828 , Prosite:IN-FAMILY:PS00475

Summary:
The L15 protein is a component of the 50S subunit of the ribosome.

L15 is a late assembly protein [Franceschi90] that appears to be required for 5S rRNA incorporation [Rohl82]. L15 interacts with domain II of 23S rRNA in a partially assembled ribosomal particle [Littlechild77, Lieberman98]. L15 appears to be dispensible for protein synthesis and cell growth [Ito84], and ribosomes lacking L15 are translationally active [Franceschi90].

L15 is a component of the binding site for erythromycin on the ribosome [Arevalo88].

L15 has RNA chaperone-like activity in an in vitro trans splicing assay [Semrad04].

Essentiality data for rplO knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L16

Synonyms: RplP

Gene: rplP Accession Numbers: EG10877 (EcoCyc), b3313, ECK3300

Locations: cytosol, ribosome

Sequence Length: 136 AAs

Molecular Weight: 15.281 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0000049 - tRNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, Remme83]
GO:0019843 - rRNA binding Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA06, GOA01, Stoffler71]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
Cellular Component: GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a]
GO:0005622 - intracellular Inferred by computational analysis [GOA01]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-35976N , EcoliWiki:b3313 , Mint:MINT-1302401 , ModBase:P0ADY7 , PR:PRO_000023822 , Pride:P0ADY7 , Protein Model Portal:P0ADY7 , RefSeq:NP_417772 , SMR:P0ADY7 , String:511145.b3313 , UniProt:P0ADY7

Relationship Links: InterPro:IN-FAMILY:IPR000114 , InterPro:IN-FAMILY:IPR016180 , InterPro:IN-FAMILY:IPR020798 , Panther:IN-FAMILY:PTHR12220 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2VHM , PDB:Structure:2VHN , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF00252 , Prints:IN-FAMILY:PR00060 , Prosite:IN-FAMILY:PS00586 , Prosite:IN-FAMILY:PS00701

Summary:
The L16 protein is a late assembly component of the 50S subunit of the ribosome; ribosomes lacking L16 are translationally active [Franceschi90]. L2 is required for assembly of L16 into the 50S subunit [Romero90].

L16 interacts with tRNA [Remme83, Maimets84, Sumpter90] and can be crosslinked to aminoacylated tRNA in the A and P site [Abdurashidova79, Osswald95]. Conserved residues within L16 were shown to be involved in the translocation of tRNA from the A to the P site [Bock13]. L16 is located within 21 Å of nucleotide C2475 of 23S rRNA, near the peptidyltransferase center [Muralikrishna95]. L16 and a histidine residue within the N-terminal domain of L16 may be important for the correct conformation of the peptidyltransferase center [Baxter80, Baxter87, Tate87]. L16 is important for release factor 2-dependent peptidyl-tRNA hydrolysis [Tate83a]. The antibiotics chloramphenicol [Nierhaus73, Pongs73] and virginiamycin S [deBethune78] interact with L16 within the ribosome.

L16 is one of six ribosomal proteins that is completely lost from ribosomes in post-stationary cells [Ramagopal84].

The N-terminal methionine of L16 appears to be methylated [Brosius76, Chen77], and additional posttranslational modifications of the protein are present [Arnold99, Nesterchuk11]. These include phosphorylation [Macek08, Soung09] as well as hydroxylation of the Arg81 residue by ribosomal protein-arginine oxygenase [Ge12].

L16 has RNA chaperone-like activity in an in vitro trans-splicing assay [Semrad04] as well as protein chaperone activity [Kovacs09].

Citations: [Czernilofsky74, Maassen74, Kazemie75, Kazemie76, Dzionara77, Pichon77, Morrison77, Hernandez77, Bernabeu77, Jaskunas77, Teraoka78, Bernabeu78, Baxter78, Spierer79, Adachi79, Marquardt79, Skold81, Guerin81, Schulze82, Moureau83, Maimets, Ganoza85, Yusupov86, Kakegawa86, Walleczek89a, Chistyakov89, Redl89, Walleczek89, RandolphAnderso89, Wower89, Vladimirov90, Sumpter91, Nag91, Agafonov97, Vladimirov00, Lancaster08]

Essentiality data for rplP knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L17

Synonyms: RplQ

Gene: rplQ Accession Numbers: EG10878 (EcoCyc), b3294, ECK3281

Locations: cytosol, ribosome

Sequence Length: 127 AAs

Molecular Weight: 14.365 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-35801N , EcoliWiki:b3294 , Mint:MINT-1251899 , ModBase:P0AG44 , PR:PRO_000023823 , Pride:P0AG44 , Protein Model Portal:P0AG44 , RefSeq:NP_417753 , SMR:P0AG44 , String:511145.b3294 , Swiss-Model:P0AG44 , UniProt:P0AG44

Relationship Links: InterPro:IN-FAMILY:IPR000456 , Panther:IN-FAMILY:PTHR14413 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF01196 , Prosite:IN-FAMILY:PS01167

Summary:
The L17 protein is a component of the 50S subunit of the ribosome.

L17 interacts directly with tRNA [Metspalu81] and can be crosslinked to 23S rRNA [Osswald90]. L17 can also be crosslinked to the spiramycin derivative dihydrospiramycin and may thus be located near the peptidyl transferase center [Bischof95].

Essentiality data for rplQ knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L18

Synonyms: RplR

Gene: rplR Accession Numbers: EG10879 (EcoCyc), b3304, ECK3291

Locations: cytosol, ribosome

Sequence Length: 117 AAs

Molecular Weight: 12.77 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-47908N , EcoliWiki:b3304 , Mint:MINT-1293631 , ModBase:P0C018 , PR:PRO_000023824 , Pride:P0C018 , Protein Model Portal:P0C018 , RefSeq:NP_417763 , SMR:P0C018 , String:511145.b3304 , UniProt:P0C018

Relationship Links: InterPro:IN-FAMILY:IPR004389 , InterPro:IN-FAMILY:IPR005484 , PDB:Structure:1ML5 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2VHM , PDB:Structure:2VHN , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3DF2 , PDB:Structure:3DF4 , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF00861

Summary:
The L18 protein is a component of the 50S subunit of the ribosome and is required for incorporation of 5S rRNA into the ribosome [Rohl82].

L18 interacts with both 23S rRNA [Osswald90] and 5S rRNA [Huber84, Newberry78, Spierer78, Fanning81]. L18 together with L5 can associate into a quaternary complex with 5S and 23S rRNAs [Spierer79]. The binding determinants of the 5S rRNA-L5-L18-L25 complex have been mapped [Peattie81, Newberry80, Speek82, Brewer83, Christiansen85, Goringer86, Gewirth88, Egebjerg89, Zhang89, Ciesiolka92, Shpanchenko96, Ostergaard98]. Iodination at a tyrosine residue abolishes binding of L18 to 5S rRNA [Fanning81a].

L18 has RNA chaperone-like activity in an in vitro trans splicing assay [Semrad04].

L18 is photoaffinity labeled by puromycin, an analog of the 3' end of aminoacylated tRNA [Bischof94]. L18 can also be crosslinked to the spiramycin derivative dihydrospiramycin and may thus be located near the peptidyl transferase center [Bischof95].

Essentiality data for rplR knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L19

Synonyms: RplS

Gene: rplS Accession Numbers: EG10880 (EcoCyc), b2606, ECK2603

Locations: cytosol, ribosome

Sequence Length: 115 AAs

Molecular Weight: 13.133 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-35793N , EcoliWiki:b2606 , Mint:MINT-1245288 , PR:PRO_000023825 , Pride:P0A7K6 , Protein Model Portal:P0A7K6 , RefSeq:NP_417097 , SMR:P0A7K6 , String:511145.b2606 , UniProt:P0A7K6

Relationship Links: InterPro:IN-FAMILY:IPR001857 , InterPro:IN-FAMILY:IPR008991 , InterPro:IN-FAMILY:IPR018257 , Panther:IN-FAMILY:PTHR15680 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2VHM , PDB:Structure:2VHN , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3DF2 , PDB:Structure:3DF4 , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF01245 , Prints:IN-FAMILY:PR00061 , Prosite:IN-FAMILY:PS01015

Summary:
The L19 protein is a component of the 50S subunit of the ribosome. Depending on the method used, L19 does [Persson95] or does not [Stoffler84] appear to be essential for viability.

L19 can be crosslinked to 23S rRNA [Bernabeu78, Skold81, Giocanti80, Osswald90], mRNA [Gimautdinova81], and ribosomal proteins S9 and L18 [Scheibe86], L3 [Walleczek89a, Walleczek89], L14 [Walleczek89a, Walleczek89], L6 [Redl89], and L25 [Walleczek89a, Redl89, Walleczek89].

L19 has RNA chaperone-like activity in an in vitro trans splicing assay [Semrad04].

L19 is photoaffinity labeled by dyhydrorosaramyicin [Siegrist85].

The phenotypes of mutants lacking L19 vary; a slow growth phenotype [Stoffler84] and accumulation of ribosome precursor particles during exponential growth and unbalanced synthesis of RNA [Wild88] have been reported.

Expression of proteins encoded by the rpsP-rimM-trmD-rplS operon does not appear to be regulated at the transcriptional level [Wikstrom88]. The lower expression levels of rimM and trmD appear to be achieved by regulating their level of translation [Wikstrom92].

Essentiality data for rplS knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L20

Synonyms: PdzA, RplT

Gene: rplT Accession Numbers: EG10881 (EcoCyc), b1716, ECK1714

Locations: cytosol, ribosome

Sequence Length: 118 AAs

Molecular Weight: 13.497 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0000027 - ribosomal large subunit assembly Inferred from experiment [Nowotny80]
GO:0006412 - translation Inferred from experiment Inferred by computational analysis [GOA01]
GO:0017148 - negative regulation of translation Inferred from experiment [Lesage92]
Molecular Function: GO:0000900 - translation repressor activity, nucleic acid binding Inferred from experiment [Lesage92]
GO:0003735 - structural constituent of ribosome Inferred from experiment Inferred by computational analysis [GOA01, Nowotny80]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a, Olsson96]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation
regulation type of regulation posttranscriptional

Unification Links: DIP:DIP-47941N , EcoliWiki:b1716 , Mint:MINT-1321645 , ModBase:P0A7L3 , PR:PRO_000023826 , Pride:P0A7L3 , Protein Model Portal:P0A7L3 , RefSeq:NP_416231 , SMR:P0A7L3 , String:511145.b1716 , UniProt:P0A7L3

Relationship Links: InterPro:IN-FAMILY:IPR005813 , Panther:IN-FAMILY:PTHR10986 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2VHM , PDB:Structure:2VHN , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3DF2 , PDB:Structure:3DF4 , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF00453 , Prints:IN-FAMILY:PR00062 , Prosite:IN-FAMILY:PS00937

Summary:
The L20 protein is a component of the 50S subunit of the ribosome and autoregulates its own expression and that of L35 at the posttranscriptional level. The N-terminal domain of L20 is required for ribosome assembly, and the C-terminal domain is required for its regulatory function [Guillier05].

L20 binds to the 5' terminal third of 23S rRNA [Spierer75, Marquardt79, Tumminia94] and is required for early assembly of the 4.3c core particle, but is not required for function of the mature 50S ribosomal subunit [Nowotny80]. L20 can replace L24 for the initiation of assembly of the 50S subunit at permissive temperatures in an L24 mutant [Franceschi88]. L20 can be crosslinked to L13 and L21 [Walleczek89a, Redl89, Walleczek89].

L20 might be required for maintaining the 50S subunit in the correct conformation for binding of aminoacyl-tRNAs [Kazemie76]. Decreasing the amount of L20 in the cell leads to a decrease in growth rate and the appearance of an aberrant ribosome peak at 41-43S [Olsson96].

Expression of rplT is autoregulated at the posttranscriptional level. L20 acts in trans at two sites, one located within infC [Lesage90] and a second located close to the translation start site of rpmI [Chiaruttini96]. The two sites may form a long-range RNA pseudoknot structure [Chiaruttini96]. Of the two L20 binding sites within the regulatory region of the mRNA, only one shows direct similarity to the L20 binding site within 23S rRNA [Guillier02]. However, both sites share secondary structure similarity with the L20 binding site in rRNA [Guillier05a]. The two binding sites interact, and only one molecule of L20 binds to the L20 mRNA [Allemand07]. Structural analysis of RNA binding by the L20 C-terminal domain by NMR show that binding of L20 to rRNA and mRNA is similar [Raibaud03]. Decreased translation of infC leads to increased L20-mediated repression of L35 expression [Chiaruttini97].

L20 directly represses the expression of rpmI, but only indirectly that of rplT, via translational coupling with rpmI [Lesage92]. A secondary structure forms between the translation initiation site of rplT and a site internal to rpmI [Lesage92]; this structure forms in vivo and is required for translational coupling [Chiaruttini96a]. It is thought that the secondary structure can form when rpmI is not translated, and it can be shown that it blocks binding of the ribosome to the ribosome binding site of rplT [Chiaruttini96a].

Unlike the regulation of the ribosomal alpha operon and of rpsO, translational autoregulation by L20 appears to be based on competition with the ribosome for binding to its mRNA [HaentjensSitri08].

Essentiality data for rplT knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L21

Synonyms: RplU

Gene: rplU Accession Numbers: EG50001 (EcoCyc), b3186, ECK3175

Locations: cytosol, ribosome

Sequence Length: 103 AAs

Molecular Weight: 11.564 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Zhang07]
GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-47852N , EcoliWiki:b3186 , Mint:MINT-1280768 , ModBase:P0AG48 , PR:PRO_000023827 , Pride:P0AG48 , Protein Model Portal:P0AG48 , RefSeq:NP_417653 , SMR:P0AG48 , String:511145.b3186 , UniProt:P0AG48

Relationship Links: InterPro:IN-FAMILY:IPR001787 , InterPro:IN-FAMILY:IPR018258 , Panther:IN-FAMILY:PTHR21349 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF00829 , Prosite:IN-FAMILY:PS01169

Summary:
The L21 protein is a component of the 50S subunit of the ribosome.

L21 interacts with 23S rRNA [Thiede98, Yamada80].

L4, L5, and L21 bind to erythromycin cooperatively [Pye90].

Essentiality data for rplU knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L22

Synonyms: EryB, RplV

Gene: rplV Accession Numbers: EG10882 (EcoCyc), b3315, ECK3302

Locations: cytosol, ribosome

Sequence Length: 110 AAs

Molecular Weight: 12.226 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
GO:0046677 - response to antibiotic Inferred by computational analysis [UniProtGOA11]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Butland05]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Zhang07]
GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a]
GO:0005622 - intracellular Inferred by computational analysis [GOA01]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0015934 - large ribosomal subunit Inferred by computational analysis [GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-35983N , EcoliWiki:b3315 , Mint:MINT-1253134 , ModBase:P61175 , PR:PRO_000023828 , Pride:P61175 , Protein Model Portal:P61175 , RefSeq:NP_417774 , SMR:P61175 , String:511145.b3315 , UniProt:P61175

Relationship Links: InterPro:IN-FAMILY:IPR001063 , InterPro:IN-FAMILY:IPR005727 , InterPro:IN-FAMILY:IPR018260 , Panther:IN-FAMILY:PTHR13501 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2VHM , PDB:Structure:2VHN , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3DF2 , PDB:Structure:3DF4 , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF00237 , Prosite:IN-FAMILY:PS00464

Summary:
The L22 protein is a component of the 50S subunit of the ribosome; it can interact with nascent translation products in the exit tunnel [Nakatogawa02] and provides one of the earliest contacts with a nascent peptide chain past the peptidyl transferase center [Houben05].

L22 is an early assembly protein and binds to the 5' end of 23S rRNA [Tumminia94, Marquardt79]; it can be crosslinked to 23S rRNA in both free ribosomes and the initiation complex [Chistyakov89]. L22 that lacks part of its extended loop that lines the peptide exit tunnel is functional in ribosome assembly [Zengel03]. L22 also crosslinks to L32 [Walleczek89a] and L18 [Redl89].

In addition to preventing elongation of the peptide chain, the antibiotic erythromycin inhibits the assembly of the 50S ribosomal subunit [Chittum95]. L22 is a component of the binding site for erythromycin on the ribosome [Arevalo88]. A 9 bp deletion in rplV, removing codons 82-84 of L22, leads to erythromycin resistance; the mutant phenotype is recessive [Chittum94]. Erythromycin-resistant L22 mutants show a perturbed conformation of 23S rRNA [Gregory99] and affect the topology of the nascent polypeptide exit tunnel [Gabashvili01].

Temperature-sensitive rplV mutants are defective in protein synthesis [BurnetteVick94, Champney80].

Essentiality data for rplV knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L23

Synonyms: RplW

Gene: rplW Accession Numbers: EG10883 (EcoCyc), b3318, ECK3305

Locations: cytosol, ribosome

Sequence Length: 100 AAs

Molecular Weight: 11.199 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Arifuzzaman06]
GO:0000166 - nucleotide binding Inferred by computational analysis [GOA01]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
Cellular Component: GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a]
GO:0005622 - intracellular Inferred by computational analysis [GOA01]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-35972N , EcoliWiki:b3318 , Mint:MINT-1225825 , ModBase:P0ADZ0 , PR:PRO_000023829 , Pride:P0ADZ0 , Protein Model Portal:P0ADZ0 , RefSeq:NP_417777 , SMR:P0ADZ0 , String:511145.b3318 , Swiss-Model:P0ADZ0 , UniProt:P0ADZ0

Relationship Links: InterPro:IN-FAMILY:IPR001014 , InterPro:IN-FAMILY:IPR012677 , InterPro:IN-FAMILY:IPR012678 , InterPro:IN-FAMILY:IPR013025 , PDB:Structure:1ML5 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2VRH , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF00276 , Prosite:IN-FAMILY:PS00050

Summary:
The L23 protein is a component of the 50S subunit of the ribosome and provides a chaperone docking site that links protein biosynthesis with protein folding. L23 is essential for growth of E. coli [Kramer02].

L23 crosslinks to Trigger Factor (TF), a protein that interacts with nascent polypeptides on the ribosome, and is essential for the association of TF with the ribosome [Kramer02, Ullers03]. It also crosslinks to the Ffh component of the Signal Recognition Particle (SRP) [Gu03, Ullers03]. Kd values for binding of TF and SRP to the ribosome under various conditions have been estimated, and TF and SRP are thought to have separate binding sites on L23 [Raine04]. L23 can also be crosslinked to a nascent peptide chain [Houben05].

L23 is an early assembly protein that interacts with 23S rRNA [Marquardt79, Osswald90, Egebjerg91, Chistyakov89, Tumminia94, Thiede98, Skold81, Vester84, Thiede98]. L23 crosslinks to tRNA in the A site [Graifer89]. L23 can also be crosslinked to L34 [Walleczek89a, Walleczek89] and L29 [Walleczek89].

L23 is photoaffinity labeled by puromycin, thus placing it within the A-site domain of the peptidyl transferase center [Cooperman75, Jaynes78, Weitzmann85]. Puromycin-crosslinked L23 interferes with tRNA binding, but 50S subunits containing it retain peptidyl transferase activity [Weitzmann90].

Reviews: [Albanese02, Ito05]

Essentiality data for rplW knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L24

Synonyms: RplX

Gene: rplX Accession Numbers: EG10884 (EcoCyc), b3309, ECK3296

Locations: cytosol, ribosome

Sequence Length: 104 AAs

Molecular Weight: 11.316 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA01]
Molecular Function: GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-47846N , EcoliWiki:b3309 , Mint:MINT-1294921 , ModBase:P60624 , PR:PRO_000023830 , Pride:P60624 , Protein Model Portal:P60624 , RefSeq:NP_417768 , SMR:P60624 , String:511145.b3309 , UniProt:P60624

Relationship Links: InterPro:IN-FAMILY:IPR003256 , InterPro:IN-FAMILY:IPR005824 , InterPro:IN-FAMILY:IPR005825 , InterPro:IN-FAMILY:IPR008991 , InterPro:IN-FAMILY:IPR014722 , Panther:IN-FAMILY:PTHR12903 , PDB:Structure:1ML5 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2VHM , PDB:Structure:2VHN , PDB:Structure:2VRH , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3DF2 , PDB:Structure:3DF4 , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF00467 , Prosite:IN-FAMILY:PS01108 , Smart:IN-FAMILY:SM00739

Summary:
The L24 protein is a component of the 50S subunit of the ribosome. L3 and L24 are the two proteins that initiate assembly of the 50S subunit; L24 is not thought to be involved in ribosomal function [Spillmann78, Nowotny82].

L24 binds directly to 23S rRNA [Tritton76, Branlant77, Egebjerg87, Osswald90, Ostergaard98]; binding of L24 together with L4 to 23S rRNA leads to a change in tertiary structure of the RNA [Stelzl01].

A mutant lacking L24 is temperature sensitive and shows a very slow growth rate [Dabbs82, Nishi85, Nishi87]. The defect is in the assembly of 50S subunits [Herold86]. Suppressors of certain temperature sensitive rplX mutations map to 23S rRNA [Nishi86] or the Lon protease [Nishi88].

L20 can replace L24 for the initiation of assembly of the 50S subunit at permissive temperatures in an L24 mutant [Franceschi88].

Essentiality data for rplX knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L25

Synonyms: RplY

Gene: rplY Accession Numbers: EG10885 (EcoCyc), b2185, ECK2179

Locations: cytosol, ribosome

Sequence Length: 94 AAs

Molecular Weight: 10.693 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11, GOA06]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0008097 - 5S rRNA binding Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-35885N , EcoliWiki:b2185 , Mint:MINT-1261165 , ModBase:P68919 , PR:PRO_000023831 , Pride:P68919 , Protein Model Portal:P68919 , RefSeq:NP_416690 , SMR:P68919 , String:511145.b2185 , UniProt:P68919

Relationship Links: InterPro:IN-FAMILY:IPR011035 , InterPro:IN-FAMILY:IPR020055 , InterPro:IN-FAMILY:IPR020056 , PDB:Structure:1B75 , PDB:Structure:1D6K , PDB:Structure:1DFU , PDB:Structure:1ML5 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2VHM , PDB:Structure:2VHN , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3DF2 , PDB:Structure:3DF4 , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:487D , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF01386 , ProDom:IN-FAMILY:PD012503

Summary:
The L25 protein is a component of the 50S subunit of the ribosome and binds to 5S rRNA.

Binding of L25 to 5S rRNA has been studied in detail [Spierer78, Huber84, Speek82, Kime83, Moore83, AbdelMeguid83, Kime84, Kime84a, Szymkowiak85, Shpanchenko96]. Solution structures of L25 alone and in complex with a segment of 5S rRNA has been determined [Stoldt98, Stoldt99], and a crystal structure of L25 bound to a fragment of 5S rRNA has been solved at 1.8 Å resolution [Lu00].

A truncated form of L25 can be detected in 2-D gels [Wasinger98].

Essentiality data for rplY knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Yamamoto09]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L27

Synonyms: Rpz, RpmA

Gene: rpmA Accession Numbers: EG50002 (EcoCyc), b3185, ECK3174

Locations: cytosol, ribosome

Sequence Length: 85 AAs

Molecular Weight: 9.124 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14]
GO:0000049 - tRNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-47933N , DisProt:DP00140 , EcoliWiki:b3185 , Mint:MINT-1317488 , PR:PRO_000023832 , Pride:P0A7L8 , Protein Model Portal:P0A7L8 , RefSeq:NP_417652 , SMR:P0A7L8 , String:511145.b3185 , UniProt:P0A7L8

Relationship Links: InterPro:IN-FAMILY:IPR001684 , InterPro:IN-FAMILY:IPR018261 , Panther:IN-FAMILY:PTHR15893 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2VHM , PDB:Structure:2VHN , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3DF2 , PDB:Structure:3DF4 , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF01016 , Prints:IN-FAMILY:PR00063 , ProDom:IN-FAMILY:PD003114 , Prosite:IN-FAMILY:PS00831

Summary:
The L27 protein is a component of the 50S subunit of the ribosome and may be an integral and functional component of the peptidyl transferase center [Hindennach71a, Chen75]. Single-molecule fluorescence resonance energy transfer studies have indicated that L27 stabilizes the peptidyl-tRNA [Wang12c].

L27 participates both in the assembly of the 50S subunit and in the peptidyl transferase reaction [Wower98, Maguire05]. L27 crosslinks to aminoacylated tRNA in the A and P site [Wower89, Parker83, Rosen93, Osswald95, Maguire05]. Involvement of L27 with the peptidyl transferase center was also suggested by its interactions with various antibiotics: N-bromoacetyl chloramphenicol, an antibiotic that interacts with the peptidyl transferase center, affinity labels L27 [Sonenberg73]. L27 is labeled by the macrolides carbomycin A, niddamycin and tylosin, which inhibit ribosomal activity [Tejedor85a]. L27 can also be crosslinked to the spiramycin derivative dihydrospiramycin [Bischof95].

L27 interacts with domain V of 23S rRNA [Osswald90, Urlaub95, Thiede98] and can be crosslinked to L33 [Redl89]. L27 is exposed on the surface of the 70S ribosome [Agafonov97].

An rpmA deletion mutant has a severe growth defect and is cold- and temperature-sensitive [Wower98]. Deleting as few as three amino acids from the amino terminus of L27 leads to a defect in peptidyl transferase activity of the resulting ribosomes [Maguire05].

Citations: [Wower95, WittmannLiebold95, Amarantos01, Maguire01, Kirillov02, Shoji11]

Essentiality data for rpmA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L28

Synonyms: RpmB

Gene: rpmB Accession Numbers: EG10886 (EcoCyc), b3637, ECK3627

Locations: cytosol, ribosome

Sequence Length: 78 AAs

Molecular Weight: 9.006 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Zheng11, Rajagopala14, Arifuzzaman06]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-35745N , EcoliWiki:b3637 , Mint:MINT-1306660 , PR:PRO_000023833 , Pride:P0A7M2 , Protein Model Portal:P0A7M2 , RefSeq:NP_418094 , SMR:P0A7M2 , String:511145.b3637 , UniProt:P0A7M2

Relationship Links: InterPro:IN-FAMILY:IPR001383 , PDB:Structure:1VT2 , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3DF2 , PDB:Structure:3DF4 , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF00830

Summary:
The L28 protein is a component of the 50S subunit of the ribosome and is required for ribosome assembly [Maguire97, Maguire97a, Maguire97b].

L28 interacts with 23S rRNA [Skold81, Osswald90, Urlaub95, Chistyakov89] and crosslinks to L9 [Walleczek89a, Redl89, Walleczek89].

L28 is labeled by the macrolides carbomycin A, niddamycin and tylosin, which inhibit ribosomal activity [Tejedor85a].

Essentiality data for rpmB knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L29

Synonyms: RpmC

Gene: rpmC Accession Numbers: EG10887 (EcoCyc), b3312, ECK3299

Locations: cytosol, ribosome

Sequence Length: 63 AAs

Molecular Weight: 7.273 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA01]
Molecular Function: GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-47911N , EcoliWiki:b3312 , Mint:MINT-1240640 , ModBase:P0A7M6 , PR:PRO_000023834 , Pride:P0A7M6 , Protein Model Portal:P0A7M6 , RefSeq:NP_417771 , SMR:P0A7M6 , String:511145.b3312 , UniProt:P0A7M6

Relationship Links: InterPro:IN-FAMILY:IPR001854 , InterPro:IN-FAMILY:IPR018254 , PDB:Structure:1ML5 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2VHM , PDB:Structure:2VHN , PDB:Structure:2VRH , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3DF2 , PDB:Structure:3DF4 , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF00831 , Prosite:IN-FAMILY:PS00579

Summary:
The L29 protein is a component of the 50S subunit of the ribosome .

L29 interacts with 23S rRNA [WittmannLiebold95, Urlaub95] and is photoaffinity labeled by puromycin, an analog of the 3' end of aminoacylated tRNA [Bischof94]. L29 crosslinks to Trigger Factor (TF) [Kramer02] and contacts the Signal Recognition Particle [Ullers03], but is not required for the association of TF with the ribosome [Kramer02].

L29 together with ACP stimulates the binding of Tn7-encoded TnsD to attTn7, the insertion site for Tn7 in the E. coli chromosome. L23 also stimulates Tn7 transposition in vitro. A mutation in L29 decreases Tn7 transposition in vivo [Sharpe98].

Essentiality data for rpmC knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L30

Synonyms: RpmD

Gene: rpmD Accession Numbers: EG10888 (EcoCyc), b3302, ECK3289

Locations: cytosol, ribosome

Sequence Length: 59 AAs

Molecular Weight: 6.542 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA01]
Molecular Function: GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
Cellular Component: GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11]
GO:0015934 - large ribosomal subunit Inferred by computational analysis [GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-35970N , EcoliWiki:b3302 , PR:PRO_000023835 , Pride:P0AG51 , Protein Model Portal:P0AG51 , RefSeq:NP_417761 , SMR:P0AG51 , String:511145.b3302 , Swiss-Model:P0AG51 , UniProt:P0AG51

Relationship Links: InterPro:IN-FAMILY:IPR005996 , InterPro:IN-FAMILY:IPR016082 , InterPro:IN-FAMILY:IPR018038 , PDB:Structure:1ML5 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF00327 , Prosite:IN-FAMILY:PS00634

Summary:
The L30 protein is a component of the 50S subunit of the ribosome.

L30 crosslinks to 23S rRNA [Osswald90]. An rpmD mutant has a growth and ribosomal assembly defect at 20°C [Geyl77].

Essentiality data for rpmD knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L31

Synonyms: RpmE

Gene: rpmE Accession Numbers: EG10889 (EcoCyc), b3936, ECK3928

Locations: cytosol, ribosome

Sequence Length: 70 AAs

Molecular Weight: 7.871 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01]
Molecular Function: GO:0008270 - zinc ion binding Inferred from experiment [Hensley12]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11]
Cellular Component: GO:0005829 - cytosol Inferred from experiment [Ishihama08]
GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a, Eistetter99]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: EcoliWiki:b3936 , ModBase:P0A7M9 , PR:PRO_000023836 , Pride:P0A7M9 , Protein Model Portal:P0A7M9 , RefSeq:NP_418371 , SMR:P0A7M9 , String:511145.b3936 , UniProt:P0A7M9

Relationship Links: InterPro:IN-FAMILY:IPR002150 , InterPro:IN-FAMILY:IPR027491 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2J28 , PDB:Structure:2RDO , PDB:Structure:2VHM , PDB:Structure:2VHN , PDB:Structure:3BBX , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J37 , Pfam:IN-FAMILY:PF01197 , Prints:IN-FAMILY:PR01249 , Prosite:IN-FAMILY:PS01143

Summary:
The L31 protein is a component of the 50S subunit of the ribosome.

L31 can be isolated in a complex with 5S rRNA and L5, L18, and L25 [Fanning81] and can be crosslinked to tRNA in the P site [Graifer89]. Modeling shows that L31 may participate in the formation, dynamics and stabilization of the S13-L5 bridge [Shasmal10]. L31 may only be loosely associated with the ribosome [Eistetter99].

L31 was found to be phosphorylated [Soung09], and the purified protein binds Zn2+ [Hensley12].

YkgM is a paralog of RpmE that has lost the predicted metal-binding "zinc ribbon" motif [Makarova01a] and was shown to lack bound Zn2+, in contrast to L31 [Hensley12]. The authors propose a model where YkgM can provide the function of L31 in the ribosome under zinc limiting conditions.

Citations: [Dabbs81a]

Essentiality data for rpmE knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 3]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 4]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 3]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L32

Synonyms: RpmF

Gene: rpmF Accession Numbers: EG10890 (EcoCyc), b1089, ECK1075

Locations: cytosol, ribosome

Sequence Length: 57 AAs

Molecular Weight: 6.446 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA01]
Molecular Function: GO:0005515 - protein binding Inferred from experiment [Rajagopala14, Arifuzzaman06]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, Zhang07]
GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11]
GO:0015934 - large ribosomal subunit Inferred by computational analysis [GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-35782N , EcoliWiki:b1089 , ModBase:P0A7N4 , PR:PRO_000023838 , Pride:P0A7N4 , Protein Model Portal:P0A7N4 , RefSeq:NP_415607 , SMR:P0A7N4 , String:511145.b1089 , UniProt:P0A7N4

Relationship Links: InterPro:IN-FAMILY:IPR002677 , InterPro:IN-FAMILY:IPR011332 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3DF2 , PDB:Structure:3DF4 , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF01783

Summary:
The L32 protein is a component of the 50S subunit of the ribosome.

L32 is located within 21 Å of nucleotide C2475 of 23S rRNA, near the peptidyltransferase center [Muralikrishna95].

Essentiality data for rpmF knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 3]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 4]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 3]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L33

Synonyms: RpmG

Gene: rpmG Accession Numbers: EG10891 (EcoCyc), b3636, ECK3626

Locations: cytosol, ribosome

Sequence Length: 55 AAs

Molecular Weight: 6.372 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA01]
Molecular Function: GO:0000049 - tRNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Hindennach71a]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: DIP:DIP-35968N , DisProt:DP00143 , EcoliWiki:b3636 , Mint:MINT-1234559 , ModBase:P0A7N9 , PR:PRO_000023839 , Pride:P0A7N9 , Protein Model Portal:P0A7N9 , RefSeq:NP_418093 , SMR:P0A7N9 , String:511145.b3636 , UniProt:P0A7N9

Relationship Links: InterPro:IN-FAMILY:IPR001705 , InterPro:IN-FAMILY:IPR011332 , InterPro:IN-FAMILY:IPR018264 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2GYA , PDB:Structure:2GYC , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2VHM , PDB:Structure:2VHN , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3DF2 , PDB:Structure:3DF4 , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF00471 , Prosite:IN-FAMILY:PS00582

Summary:
The L33 protein is a component of the 50S subunit of the ribosome.

L33 is located within 21 Å of nucleotide C2475 of 23S rRNA, near the peptidyltransferase center [Muralikrishna95]. L33 had previously been shown to crosslink to 23S rRNA [Osswald90] and to tRNA in the P site [Bausk85, Graifer89, Podkowinski89, Sumpter90, Podkowinski91, Mitchell93, Osswald95] and E site [Osswald95]. L33 also crosslinks to L1 and L27 [Walleczek89a, Redl89, Walleczek89].

The initiating methionine of L33 is lost [Arnold99] or may be methylated [Chang77]; L33 is methylated at the first alanine residue [Cammack65, Chang77, Arnold99].

A strain containing an IS element insertion in rpmG shows no major defect in ribosome assembly [Coleman93]; L33 appears to have no significant role in ribosome synthesis or function [Maguire97, Maguire97a, Maguire97b].

Essentiality data for rpmG knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 3]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 4]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 3]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L34

Synonyms: SsaF, RimA, RpmH

Gene: rpmH Accession Numbers: EG10892 (EcoCyc), b3703, ECK3695

Locations: cytosol, ribosome

Sequence Length: 46 AAs

Molecular Weight: 5.38 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA01]
Molecular Function: GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation
regulation type of regulation posttranscriptional inhibition / activation of enzymes

Unification Links: EcoliWiki:b3703 , PR:PRO_000023840 , Pride:P0A7P5 , Protein Model Portal:P0A7P5 , RefSeq:NP_418158 , SMR:P0A7P5 , String:511145.b3703 , UniProt:P0A7P5

Relationship Links: InterPro:IN-FAMILY:IPR000271 , InterPro:IN-FAMILY:IPR020939 , Panther:IN-FAMILY:PTHR14503 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2VHM , PDB:Structure:2VHN , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3DF2 , PDB:Structure:3DF4 , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF00468 , ProDom:IN-FAMILY:PD003101 , Prosite:IN-FAMILY:PS00784

Summary:
The L34 protein is a component of the 50S subunit of the ribosome. L34 was also identified as antizyme 2, an inhibitor of the biosynthetic ornithine and arginine decarboxylases; these enzymes are involved in the biosynthesis of polyamine [Panagiotidis84].

L34 physically interacts with ornithine and arginine decarboxylase, and overexpression of L34 decreases the production of polyamine in vivo [Panagiotidis95]. Levels of L34 increase in response to polyamines; the effect is thought to be due to an increase in the level of transcription of rpmH [Huang90].

The rimA mutant, likely an allele of rpmH [Hansen82], has a cold-sensitive growth and ribosome assembly defect [Bryant74].

Reviews: [Canellakis85, Panagiotidis88].

Essentiality data for rpmH knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Comment 2]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L35

Synonyms: RpmI, 50S ribosomal subunit protein A, X1 protein

Gene: rpmI Accession Numbers: EG11231 (EcoCyc), b1717, ECK1715

Locations: cytosol, ribosome

Sequence Length: 65 AAs

Molecular Weight: 7.289 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA01]
Molecular Function: GO:0003735 - structural constituent of ribosome Inferred from experiment Inferred by computational analysis [GOA01, Wada87]
Cellular Component: GO:0022625 - cytosolic large ribosomal subunit Inferred from experiment [Wada87]
GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: EcoliWiki:b1717 , PR:PRO_000023841 , Pride:P0A7Q1 , Protein Model Portal:P0A7Q1 , RefSeq:NP_416232 , SMR:P0A7Q1 , String:511145.b1717 , UniProt:P0A7Q1

Relationship Links: InterPro:IN-FAMILY:IPR001706 , InterPro:IN-FAMILY:IPR018265 , InterPro:IN-FAMILY:IPR021137 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2VHM , PDB:Structure:2VHN , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3DF2 , PDB:Structure:3DF4 , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF01632 , Prints:IN-FAMILY:PR00064 , Prosite:IN-FAMILY:PS00936

Summary:
The L35 protein is a component of the 50S subunit of the ribosome [Wada87].

L35 can be crosslinked to the spiramycin derivative dihydrospiramycin and may thus be located near the peptidyl transferase center [Bischof95].

Essentiality data for rpmI knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 3]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 4]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 3]

Subunit of 50S ribosomal subunit: 50S ribosomal subunit protein L36

Synonyms: SecX, RpmJ, 50S ribosomal subunit protein B

Gene: rpmJ Accession Numbers: EG11232 (EcoCyc), b3299, ECK3286

Locations: cytosol, ribosome

Sequence Length: 38 AAs

Molecular Weight: 4.364 kD (from nucleotide sequence)

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA01]
Molecular Function: GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]
GO:0005840 - ribosome Inferred by computational analysis [UniProtGOA11, GOA01]
GO:0022625 - cytosolic large ribosomal subunit
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11]

MultiFun Terms: cell structure ribosomes
information transfer protein related ribosomal proteins
information transfer protein related translation

Unification Links: EcoliWiki:b3299 , PR:PRO_000023842 , Protein Model Portal:P0A7Q6 , RefSeq:NP_417758 , SMR:P0A7Q6 , String:511145.b3299 , UniProt:P0A7Q6

Relationship Links: InterPro:IN-FAMILY:IPR000473 , Panther:IN-FAMILY:PTHR18804 , PDB:Structure:1P85 , PDB:Structure:1P86 , PDB:Structure:1VS6 , PDB:Structure:1VS8 , PDB:Structure:1VT2 , PDB:Structure:2AW4 , PDB:Structure:2AWB , PDB:Structure:2I2T , PDB:Structure:2I2V , PDB:Structure:2J28 , PDB:Structure:2QAM , PDB:Structure:2QAO , PDB:Structure:2QBA , PDB:Structure:2QBC , PDB:Structure:2QBE , PDB:Structure:2QBG , PDB:Structure:2QBI , PDB:Structure:2QBK , PDB:Structure:2QOV , PDB:Structure:2QOX , PDB:Structure:2QOZ , PDB:Structure:2QP1 , PDB:Structure:2RDO , PDB:Structure:2VHM , PDB:Structure:2VHN , PDB:Structure:2WWQ , PDB:Structure:2Z4L , PDB:Structure:2Z4N , PDB:Structure:3BBX , PDB:Structure:3DF2 , PDB:Structure:3DF4 , PDB:Structure:3E1B , PDB:Structure:3E1D , PDB:Structure:3FIK , PDB:Structure:3I1N , PDB:Structure:3I1P , PDB:Structure:3I1R , PDB:Structure:3I1T , PDB:Structure:3I20 , PDB:Structure:3I22 , PDB:Structure:3IZT , PDB:Structure:3IZU , PDB:Structure:3J01 , PDB:Structure:3J0T , PDB:Structure:3J0W , PDB:Structure:3J0Y , PDB:Structure:3J11 , PDB:Structure:3J12 , PDB:Structure:3J14 , PDB:Structure:3J19 , PDB:Structure:3J37 , PDB:Structure:3KCR , PDB:Structure:3OAS , PDB:Structure:3OAT , PDB:Structure:3OFC , PDB:Structure:3OFD , PDB:Structure:3OFQ , PDB:Structure:3OFR , PDB:Structure:3OFZ , PDB:Structure:3OG0 , PDB:Structure:3ORB , PDB:Structure:3R8S , PDB:Structure:3R8T , PDB:Structure:3SGF , PDB:Structure:3UOS , PDB:Structure:4GAR , PDB:Structure:4GAU , PDB:Structure:4KIX , PDB:Structure:4KIZ , PDB:Structure:4KJ1 , PDB:Structure:4KJ3 , PDB:Structure:4KJ5 , PDB:Structure:4KJ7 , PDB:Structure:4KJ9 , PDB:Structure:4KJB , Pfam:IN-FAMILY:PF00444 , Prosite:IN-FAMILY:PS00828

Summary:
The L36 protein is a component of the 50S subunit of the ribosome [Wada87]. L36 is highly conserved in bacteria, mitochondria and chloroplasts, but not present in archaea and eucarya [Maeder05].

Ribosomes lacking L36 are correctly assembled. However, chemical protection experiments suggest that rRNA tertiary interactions are disrupted in ribosomes lacking L36, thus arguing that L36 plays a significant role in organizing 23S rRNA structure [Maeder05]. L36 has ben shown to crosslink to 23S rRNA [Urlaub95].

Deletion of rpmJ causes a temperature-sensitive growth defect [Ikegami05, Maeder05]; the rpmJ deletion led to decreased expression of secY, located immediately upstream of rpmJ. rpmJ does not appear to be essential for protein synthesis [Ikegami05].

Essentiality data for rpmJ knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 3]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 4]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 3]

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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