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Escherichia coli K-12 substr. MG1655 Polypeptide: 50S ribosomal subunit protein L25



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

Regulation Summary Diagram: ?

Component of:
50S ribosomal subunit
ribosome (summary available)

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, Moore83a, 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 [Lu00a].

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

Locations: cytosol, ribosome

Map Position: [2,280,539 -> 2,280,823] (49.15 centisomes)
Length: 285 bp / 94 aa

Molecular Weight of Polypeptide: 10.693 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0007231 , CGSC:242 , DIP:DIP-35885N , EchoBASE:EB0878 , EcoGene:EG10885 , EcoliWiki:b2185 , Mint:MINT-1261165 , ModBase:P68919 , OU-Microarray:b2185 , PortEco:rplY , PR:PRO_000023831 , Pride:P68919 , Protein Model Portal:P68919 , RefSeq:NP_416690 , RegulonDB:EG10885 , 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

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0006412 - translation Inferred by computational analysis [GOA06, GOA01a]
Molecular Function: GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01a]
GO:0008097 - 5S rRNA binding Inferred by computational analysis [GOA01a]
GO:0019843 - rRNA binding Inferred by computational analysis [UniProtGOA11a]
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 [UniProtGOA11a, GOA01a]
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [UniProtGOA11a]

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

Essentiality data for rplY knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox No 37 Aerobic 7   No [Baba06, Yamamoto09a]

Credits:
Last-Curated ? 19-May-2006 by Keseler I , SRI International


Subunit of: 50S ribosomal subunit

Synonyms: ribosome, large subunit

Subunit composition of 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)

Component of: ribosome (summary available)

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

Credits:
Created 02-Jun-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
Sequence-Conflict 86 -> 94
[Richterich93, UniProt10]
Alternate sequence: LQHIDFVRA → CSTSTSFALNC; UniProt: (in Ref. 6; AAA16413);


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

History:
10/20/97 Gene b2185 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10885; confirmed by SwissProt match.


References

AbdelMeguid83: Abdel-Meguid SS, Moore PB, Steitz TA (1983). "Crystallization of a ribonuclease-resistant fragment of Escherichia coli 5 S ribosomal RNA and its complex with protein L25." J Mol Biol 171(2);207-15. PMID: 6197527

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

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

GOA01a: 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

Hindennach71a: Hindennach I, Kaltschmidt E, Wittmann HG (1971). "Ribosomal proteins. Isolation of proteins from 50S ribosomal subunits of Escherichia coli." Eur J Biochem 23(1);12-6. PMID: 4942547

Huber84: Huber PW, Wool IG (1984). "Nuclease protection analysis of ribonucleoprotein complexes: use of the cytotoxic ribonuclease alpha-sarcin to determine the binding sites for Escherichia coli ribosomal proteins L5, L18, and L25 on 5S rRNA." Proc Natl Acad Sci U S A 81(2);322-6. PMID: 6364140

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

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

Kime83: Kime MJ, Moore PB (1983). "Nuclear Overhauser experiments at 500 MHz on the downfield proton spectra of 5S ribonucleic acid and its complex with ribosomal protein L25." Biochemistry 22(11);2622-9. PMID: 6347250

Kime84: Kime MJ, Moore PB (1984). "Escherichia coli ribosomal 5S RNA-protein L25 nucleoprotein complex: effects of RNA binding on the protein structure and the nature of the interaction." Biochemistry 23(8);1688-95. PMID: 6372859

Kime84a: Kime MJ (1984). "Assignment of resonances of exchangeable protons in the NMR spectrum of the complex formed by Escherichia coli ribosomal protein L25 and uniformly nitrogen-15 enriched 5 S RNA fragment." FEBS Lett 175(2);259-62. PMID: 6383867

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

Lu00a: Lu M, Steitz TA (2000). "Structure of Escherichia coli ribosomal protein L25 complexed with a 5S rRNA fragment at 1.8-A resolution." Proc Natl Acad Sci U S A 97(5);2023-8. PMID: 10696113

Moore83a: Moore PB, Kime MJ, Leontis NB, Abdel-Meguid SS (1983). "Physical studies on a nucleoprotein from the ribosome of E. coli." J Biomol Struct Dyn 1(2);383-94. PMID: 6401116

Ogle05: Ogle JM, Ramakrishnan V (2005). "Structural insights into translational fidelity." Annu Rev Biochem 74;129-77. PMID: 15952884

Ramakrishnan02: Ramakrishnan V (2002). "Ribosome structure and the mechanism of translation." Cell 108(4);557-72. PMID: 11909526

Richterich93: Richterich P., Lakey N., Gryan G., Jaehn L., Mintz L., Robison K., Church G.M. (1993). "Automated multiplex sequencing of the E.coli genome." Data submission to EMBL/GenBank/DDBJ databases on 1993-10.

Schuwirth05: Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, Holton JM, Cate JH (2005). "Structures of the bacterial ribosome at 3.5 A resolution." Science 310(5749);827-34. PMID: 16272117

Shpanchenko96: Shpanchenko OV, Zvereva MI, Dontsova OA, Nierhaus KH, Bogdanov AA (1996). "5S rRNA sugar-phosphate backbone protection in complexes with specific ribosomal proteins." FEBS Lett 394(1);71-5. PMID: 8925931

Speek82: Speek M, Lind A (1982). "Structural analyses of E. coli 5S RNA fragments, their associates and complexes with proteins L18 and L25." Nucleic Acids Res 10(3);947-63. PMID: 6278442

Spierer78: Spierer P, Zimmermann RA (1978). "Stoichiometry, cooperativity, and stability of interactions between 5S RNA and proteins L5, L18, and L25 from the 50S ribosomal subunit of Escherichia coli." Biochemistry 17(13);2474-9. PMID: 354687

Stoldt98: Stoldt M, Wohnert J, Gorlach M, Brown LR (1998). "The NMR structure of Escherichia coli ribosomal protein L25 shows homology to general stress proteins and glutaminyl-tRNA synthetases." EMBO J 17(21);6377-84. PMID: 9799245

Stoldt99: Stoldt M, Wohnert J, Ohlenschlager O, Gorlach M, Brown LR (1999). "The NMR structure of the 5S rRNA E-domain-protein L25 complex shows preformed and induced recognition." EMBO J 18(22);6508-21. PMID: 10562563

Szymkowiak85: Szymkowiak C, Wagner R (1985). "Analysis of a sequence region of 5S RNA from E. coli cross-linked in situ to the ribosomal protein L25." Nucleic Acids Res 13(11);3953-68. PMID: 3892485

UniProt10: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

Wasinger98: Wasinger VC, Humphery-Smith I (1998). "Small genes/gene-products in Escherichia coli K-12." FEMS Microbiol Lett 169(2);375-82. PMID: 9868784

Yamamoto09a: Yamamoto N, Nakahigashi K, Nakamichi T, Yoshino M, Takai Y, Touda Y, Furubayashi A, Kinjyo S, Dose H, Hasegawa M, Datsenko KA, Nakayashiki T, Tomita M, Wanner BL, Mori H (2009). "Update on the Keio collection of Escherichia coli single-gene deletion mutants." Mol Syst Biol 5;335. PMID: 20029369

Yonath05: Yonath A (2005). "Antibiotics targeting ribosomes: resistance, selectivity, synergism and cellular regulation." Annu Rev Biochem 74;649-79. PMID: 16180279

Zhang09b: Zhang W, Dunkle JA, Cate JH (2009). "Structures of the ribosome in intermediate states of ratcheting." Science 325(5943);1014-7. PMID: 19696352


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 18.5 on Mon Dec 22, 2014, BIOCYC13A.