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Escherichia coli K-12 substr. MG1655 Polypeptide: 30S ribosomal subunit protein S4



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

Synonyms: ramA, sud(2), sud2

Regulation Summary Diagram: ?

Component of:
30S ribosomal subunit (summary available)
ribosome (summary available)

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 [Chen10a]. 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]

Gene Citations: [Post80, Jaskunas75]

Locations: cytosol, ribosome

Map Position: [3,439,077 <- 3,439,697] (74.12 centisomes)
Length: 621 bp / 206 aa

Molecular Weight of Polypeptide: 23.469 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0010805 , CGSC:227 , DIP:DIP-35794N , EchoBASE:EB0896 , EcoGene:EG10903 , EcoliWiki:b3296 , Mint:MINT-6478162 , OU-Microarray:b3296 , PortEco:rpsD , PR:PRO_000023857 , Pride:P0A7V8 , Protein Model Portal:P0A7V8 , RefSeq:NP_417755 , RegulonDB:EG10903 , 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

Gene-Reaction Schematic: ?

Genetic Regulation Schematic: ?

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

Regulated Transcription Units (2 total): ?

Notes:

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 1]

Credits:
Last-Curated ? 08-May-2013 by Keseler I , SRI International


Subunit of: 30S ribosomal subunit

Synonyms: ribosome, small subunit

Subunit composition of 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]
         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)

Component of: ribosome (summary available)

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].

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

Enzymes activated by 30S ribosomal subunit, sorted by the type of activation, are:

Activator (Mechanism unknown) of: GTPase [Daigle04, Himeno04]

Credits:
Created 28-Mar-2006 by Keseler I , SRI International


Subunit of: 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 [Zhang09b, 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

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


Sequence Features

Feature Class Location Citations Comment
Cleavage-of-Initial-Methionine 1
[Schiltz75, Reinbolt73, UniProt11]
UniProt: Removed.
Chain 2 -> 206
[UniProt09]
UniProt: 30S ribosomal protein S4;
Mutagenesis-Variant 44 -> 47
[UniProt10a]
Alternate sequence: RKPR → AKPA; UniProt: Decreases mRNA unwinding ability of the ribosome;
Extrinsic-Sequence-Variant 51
[UniProt10a]
Alternate sequence: Y → D; UniProt: (in rpsD101; suppresses a temperature-sensitive mutant of release factor 1, R137P. Not a ram mutation);
Sequence-Conflict 91
[Schiltz75, Reinbolt73, UniProt10a]
Alternate sequence: L → missing; UniProt: (in Ref. 4; AA sequence and 5; AA sequence);
Sequence-Conflict 95
[Schiltz75, Reinbolt73, UniProt10a]
Alternate sequence: E → Q; UniProt: (in Ref. 4; AA sequence and 5; AA sequence);
Conserved-Region 96 -> 156
[UniProt09]
UniProt: S4 RNA-binding;
Sequence-Conflict 138 -> 144
[Schiltz75, Reinbolt73, UniProt10a]
Alternate sequence: SPNDVVS → DPNSVV; UniProt: (in Ref. 4; AA sequence and 5; AA sequence);
Sequence-Conflict 152
[Schiltz75, Reinbolt73, UniProt10a]
Alternate sequence: Q → E; UniProt: (in Ref. 4; AA sequence and 5; AA sequence);
Sequence-Conflict 166
[Schiltz75, Reinbolt73, UniProt10a]
Alternate sequence: E → Q; UniProt: (in Ref. 4; AA sequence and 5; AA sequence);
Acetylation-Modification 167
[Yu08]
 
Extrinsic-Sequence-Variant 170 -> 206
[UniProt10a]
Alternate sequence: WLEVDAGKMEGTFKRKPERSDLSADINEHLIVELYSK → missing; UniProt: (in rpsD16; suppresses streptomycin dependence in protein S12. A ram mutation);
Extrinsic-Sequence-Variant 177 -> 206
[UniProt10a]
Alternate sequence: KMEGTFKRKPERSDLSADINEHLIVELYSK → GRYV; UniProt: (in rpsD12; suppresses streptomycin dependence in protein S12. A ram mutation);
Extrinsic-Sequence-Variant 179 -> 206
[UniProt10a]
Alternate sequence: EGTFKRKPERSDLSADINEHLIVELYSK → ARYV; UniProt: (in rpsD14; suppresses streptomycin dependence in protein S12. A ram mutation);


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
10/20/97 Gene b3296 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10903; confirmed by SwissProt match.


References

Adilakshmi08: Adilakshmi T, Bellur DL, Woodson SA (2008). "Concurrent nucleation of 16S folding and induced fit in 30S ribosome assembly." Nature 455(7217);1268-72. PMID: 18784650

Andersson82: Andersson DI, Bohman K, Isaksson LA, Kurland CG (1982). "Translation rates and misreading characteristics of rpsD mutants in Escherichia coli." Mol Gen Genet 187(3);467-72. PMID: 6757661

Andersson83: Andersson DI, Kurland CG (1983). "Ram ribosomes are defective proofreaders." Mol Gen Genet 191(3);378-81. PMID: 6355760

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Baker95: Baker AM, Draper DE (1995). "Messenger RNA recognition by fragments of ribosomal protein S4." J Biol Chem 270(39);22939-45. PMID: 7559430

Balashov03: Balashov S, Humayun MZ (2003). "Escherichia coli cells bearing a ribosomal ambiguity mutation in rpsD have a mutator phenotype that correlates with increased mistranslation." J Bacteriol 185(16);5015-8. PMID: 12897024

Bedwell85: Bedwell D, Davis G, Gosink M, Post L, Nomura M, Kestler H, Zengel JM, Lindahl L (1985). "Nucleotide sequence of the alpha ribosomal protein operon of Escherichia coli." Nucleic Acids Res 1985;13(11);3891-903. PMID: 2989779

Bellur09: Bellur DL, Woodson SA (2009). "A minimized rRNA-binding site for ribosomal protein S4 and its implications for 30S assembly." Nucleic Acids Res 37(6);1886-96. PMID: 19190093

Chen10a: Chen K, Eargle J, Sarkar K, Gruebele M, Luthey-Schulten Z (2010). "Functional role of ribosomal signatures." Biophys J 99(12);3930-40. PMID: 21156135

Conrad87: Conrad RC, Craven GR (1987). "A cyanogen bromide fragment of S4 that specifically rebinds 16S RNA." Nucleic Acids Res 15(24);10331-43. PMID: 3697092

Daigle04: Daigle DM, Brown ED (2004). "Studies of the interaction of Escherichia coli YjeQ with the ribosome in vitro." J Bacteriol 186(5);1381-7. PMID: 14973029

Deckman85: Deckman IC, Draper DE (1985). "Specific interaction between ribosomal protein S4 and the alpha operon messenger RNA." Biochemistry 24(27);7860-5. PMID: 3912010

Deckman87: Deckman IC, Draper DE, Thomas MS (1987). "S4-alpha mRNA translation repression complex. I. Thermodynamics of formation." J Mol Biol 196(2);313-22. PMID: 2443719

Deckman87a: Deckman IC, Draper DE (1987). "S4-alpha mRNA translation regulation complex. II. Secondary structures of the RNA regulatory site in the presence and absence of S4." J Mol Biol 196(2);323-32. PMID: 2443720

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

Dunkle11: Dunkle JA, Wang L, Feldman MB, Pulk A, Chen VB, Kapral GJ, Noeske J, Richardson JS, Blanchard SC, Cate JH (2011). "Structures of the bacterial ribosome in classical and hybrid states of tRNA binding." Science 332(6032);981-4. PMID: 21596992

Gluick95: Gluick TC, Gerstner RB, Draper DE (1995). "A conformational switch in a regulated mRNA involves tertiary structure." Nucleic Acids Symp Ser (33);200-2. PMID: 8643369

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Hensley11: Hensley MP, Tierney DL, Crowder MW (2011). "Zn(II) binding to Escherichia coli 70S ribosomes." Biochemistry 50(46);9937-9. PMID: 22026583

Himeno04: Himeno H, Hanawa-Suetsugu K, Kimura T, Takagi K, Sugiyama W, Shirata S, Mikami T, Odagiri F, Osanai Y, Watanabe D, Goto S, Kalachnyuk L, Ushida C, Muto A (2004). "A novel GTPase activated by the small subunit of ribosome." Nucleic Acids Res 32(17);5303-9. PMID: 15466596

Hindennach71: Hindennach I, Stoffler G, Wittmann HG (1971). "Ribosomal proteins. Isolation of the proteins from 30S ribosomal subunits of Escherichia coli." Eur J Biochem 23(1);7-11. PMID: 4942549

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

Jaskunas75: Jaskunas SR, Burgess RR, Nomura M (1975). "Identification of a gene for the alpha-subunit of RNA polymerase at the str-spc region of the Escherichia coli chromosome." Proc Natl Acad Sci U S A 72(12);5036-40. PMID: 1108010

JinksRobertson82: Jinks-Robertson S, Nomura M (1982). "Ribosomal protein S4 acts in trans as a translational repressor to regulate expression of the alpha operon in Escherichia coli." J Bacteriol 151(1);193-202. PMID: 6211432

Kaczanowska07: Kaczanowska M, Ryden-Aulin M (2007). "Ribosome biogenesis and the translation process in Escherichia coli." Microbiol Mol Biol Rev 71(3);477-94. PMID: 17804668

Kuhlenkoetter11: Kuhlenkoetter S, Wintermeyer W, Rodnina MV (2011). "Different substrate-dependent transition states in the active site of the ribosome." Nature 476(7360);351-4. PMID: 21804565

Mayerle11: Mayerle M, Bellur DL, Woodson SA (2011). "Slow formation of stable complexes during coincubation of minimal rRNA and ribosomal protein S4." J Mol Biol 412(3);453-65. PMID: 21821049

Meek84: Meek DW, Hayward RS (1984). "Nucleotide sequence of the rpoA-rplQ DNA of Escherichia coli: a second regulatory binding site for protein S4?." Nucleic Acids Res 1984;12(14);5813-21. PMID: 6379605

Milon12: Milon P, Maracci C, Filonava L, Gualerzi CO, Rodnina MV (2012). "Real-time assembly landscape of bacterial 30S translation initiation complex." Nat Struct Mol Biol 19(6);609-15. PMID: 22562136

Mizushima70: Mizushima S, Nomura M (1970). "Assembly mapping of 30S ribosomal proteins from E. coli." Nature 226(5252);1214. PMID: 4912319

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Other References Related to Gene Regulation

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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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