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MetaCyc Polypeptide: 50S ribosomal subunit protein L25

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

Species: Escherichia coli K-12 substr. MG1655

Component of:
50S ribosomal subunit
ribosome

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 [Lu00].

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

Locations: cytosol, ribosome

Map Position: [2,280,539 -> 2,280,823]

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:b2185 , 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

Ortholog Links: Ecol199310Cyc (Escherichia coli CFT073):C2722 , EcoO157Cyc (Escherichia coli O157:H7 str. EDL933):RPLY , ShigellaCyc (Shigella flexneri 2a str. 2457T):RPLY

Gene-Reaction Schematic: ?

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 [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

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


Subunit of: 50S ribosomal subunit

Synonyms: ribosome, large subunit

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of 50S ribosomal subunit = [RplA][RplB][RplC][RplD][RplE][RplF][(RplJ)([RplL]2)2][RplI][RplJ][RplK][RplM][RplN][RplO][RplP][RplQ][RplR][RplS][RplT][RplU][RplV][RplW][RplX][RplY][RpmA][RpmB][RpmC][RpmD][RpmE][RpmF][RpmG][RpmH][RpmI][RpmJ][5S ribosomal RNA (rrfA)][23S ribosomal RNA (rrlA)]
         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
                 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 L10 = RplJ (extended 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

Credits:
Created 02-Jun-2006 by Keseler I , SRI International


Subunit of: ribosome

Species: Escherichia coli K-12 substr. MG1655

Subunit composition of ribosome = [(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))][(RplA)(RplB)(RplC)(RplD)(RplE)(RplF)([RplJ][(RplL)2]2)(RplI)(RplJ)(RplK)(RplM)(RplN)(RplO)(RplP)(RplQ)(RplR)(RplS)(RplT)(RplU)(RplV)(RplW)(RplX)(RplY)(RpmA)(RpmB)(RpmC)(RpmD)(RpmE)(RpmF)(RpmG)(RpmH)(RpmI)(RpmJ)(5S ribosomal RNA (rrfA))(23S ribosomal RNA (rrlA))]
         30S ribosomal subunit = (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))
                 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 = (RplA)(RplB)(RplC)(RplD)(RplE)(RplF)([RplJ][(RplL)2]2)(RplI)(RplJ)(RplK)(RplM)(RplN)(RplO)(RplP)(RplQ)(RplR)(RplS)(RplT)(RplU)(RplV)(RplW)(RplX)(RplY)(RpmA)(RpmB)(RpmC)(RpmD)(RpmE)(RpmF)(RpmG)(RpmH)(RpmI)(RpmJ)(5S ribosomal RNA (rrfA))(23S ribosomal RNA (rrlA))
                 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
                         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 L10 = RplJ (extended 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)

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


Sequence Features

Feature Class Location Citations Comment
Sequence-Conflict 86 -> 94
[Richterich93, UniProt10a]
Alternate sequence: CSTSTSFALNC; UniProt: (in Ref. 6; AAA16413);

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

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

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."

Hindennach71: 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

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

Lu00: 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

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.

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);947-65. 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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

UniProtGOA11: 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


Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of MetaCyc: Caspi et al, Nucleic Acids Research 42:D459-D471 2014
Page generated by SRI International Pathway Tools version 18.5 on Mon Dec 22, 2014, biocyc14.