Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
twitter

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, Kime83a, Moore83, AbdelMeguid83, Kime84a, Kime84b, 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 [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

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."

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

Kime83a: 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

Kime84a: 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

Kime84b: 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

Moore83: 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 Fri Nov 28, 2014, biocyc13.