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MetaCyc Polypeptide: 50S ribosomal subunit protein L31

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

Species: Escherichia coli K-12 substr. MG1655

Component of:
50S ribosomal subunit
ribosome

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: [Dabbs81]

Locations: cytosol, ribosome

Map Position: [4,125,036 -> 4,125,248]

Unification Links: ASAP:ABE-0012867 , CGSC:237 , EchoBASE:EB0882 , EcoGene:EG10889 , EcoliWiki:b3936 , ModBase:P0A7M9 , OU-Microarray:b3936 , PortEco:b3936 , PR:PRO_000023836 , Pride:P0A7M9 , Protein Model Portal:P0A7M9 , RefSeq:NP_418371 , RegulonDB:EG10889 , 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

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

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 [GOA00]
GO:0003735 - structural constituent of ribosome Inferred by computational analysis [GOA01]
GO:0008270 - zinc ion binding Inferred by computational analysis [GOA00]
GO:0019843 - rRNA binding Inferred by computational analysis [GOA00]
GO:0046872 - metal ion binding Inferred by computational analysis [GOA00]
Cellular Component: GO:0005829 - cytosol
GO:0005840 - ribosome Inferred by computational analysis [GOA01, GOA00]
GO:0022625 - cytosolic large ribosomal subunit
GO:0030529 - ribonucleoprotein complex Inferred by computational analysis [GOA00]

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

Credits:
Last-Curated ? 31-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
Acetylation-Modification 8
[Zhang09a, UniProt11]
UniProt: N6-acetyllysine.
Mutagenesis-Variant 16
[Hensley12, UniProt14]
Alternate sequence: S; UniProt: No Zn(2+) binding.
Metal-Binding-Site 16
[UniProt10]
UniProt: Zinc; Non-Experimental Qualifier: by similarity;
Mutagenesis-Variant 18
[Hensley12, UniProt14]
Alternate sequence: S; UniProt: Binds Zn(2+) normally.
Mutagenesis-Variant 37 -> 40
[Hensley12, UniProt14]
Alternate sequence: SSKS; UniProt: Binds Zn(2+) normally.

History:
10/20/97 Gene b3936 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10889.


References

Dabbs81: Dabbs ER (1981). "The gene for ribosomal protein L31, rpmE, is located at 88.5 minutes on the Escherichia coli chromosomal linkage map." J Bacteriol 148(1);379-82. PMID: 7026537

Eistetter99: Eistetter AJ, Butler PD, Traut RR, Fanning TG (1999). "Characterization of Escherichia coli 50S ribosomal protein L31." FEMS Microbiol Lett 180(2);345-9. PMID: 10556732

Fanning81: Fanning TG, Traut RR (1981). "Topography of the C. coli 5S RNA-protein complex as determined by crosslinking with dimethyl suberimidate and dimethyl-3,3'-dithiobispropionimidate." Nucleic Acids Res 9(4);993-1004. PMID: 7015289

GOA00: GOA (2000). "Gene Ontology annotation based on Swiss-Prot keyword mapping."

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."

Graifer89: Graifer DM, Babkina GT, Matasova NB, Vladimirov SN, Karpova GG, Vlassov VV (1989). "Structural arrangement of tRNA binding sites on Escherichia coli ribosomes, as revealed from data on affinity labelling with photoactivatable tRNA derivatives." Biochim Biophys Acta 1008(2);146-56. PMID: 2660905

Hensley12: Hensley MP, Gunasekera TS, Easton JA, Sigdel TK, Sugarbaker SA, Klingbeil L, Breece RM, Tierney DL, Crowder MW (2012). "Characterization of Zn(II)-responsive ribosomal proteins YkgM and L31 in E. coli." J Inorg Biochem 111;164-72. PMID: 22196016

Makarova01a: Makarova KS, Ponomarev VA, Koonin EV (2001). "Two C or not two C: recurrent disruption of Zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins." Genome Biol 2(9);RESEARCH 0033. PMID: 11574053

Shasmal10: Shasmal M, Chakraborty B, Sengupta J (2010). "Intrinsic molecular properties of the protein-protein bridge facilitate ratchet-like motion of the ribosome." Biochem Biophys Res Commun 399(2);192-7. PMID: 20643101

Soung09: Soung GY, Miller JL, Koc H, Koc EC (2009). "Comprehensive analysis of phosphorylated proteins of Escherichia coli ribosomes." J Proteome Res 8(7);3390-402. PMID: 19469554

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt11: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt14: UniProt Consortium (2014). "UniProt version 2014-01 released on 2014-01-01 00:00:00." Database.

Zhang09a: Zhang J, Sprung R, Pei J, Tan X, Kim S, Zhu H, Liu CF, Grishin NV, Zhao Y (2009). "Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli." Mol Cell Proteomics 8(2);215-25. PMID: 18723842


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 Thu Nov 27, 2014, BIOCYC14B.