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Protein

Ribosomal protein S6--L-glutamate ligase

Gene

rimK

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Is an L-glutamate ligase that catalyzes the ATP-dependent post-translational addition of glutamate residues to the C-terminus of ribosomal protein S6 (RpsF). Is also able to catalyze the synthesis of poly-alpha-glutamate in vitro, via ATP hydrolysis from unprotected glutamate as substrate. The number of glutamate residues added to either RpsF or to poly-alpha-glutamate changes with pH.UniRule annotation2 Publications

Cofactori

Mg2+UniRule annotation, Mn2+UniRule annotationNote: Binds 2 magnesium or manganese ions per subunit.UniRule annotation

pH dependencei

Optimum pH is 9.5 for RpsF modification and 9 for polyglutamate synthase activity.1 Publication

Temperature dependencei

Shows thermal stability. Exhibits 86% activity after incubation at 55 degrees Celsius for 15 minutes, but its activity decreases sharply at 60 degrees Celsius.1 Publication

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Binding sitei141 – 1411ATP1 Publication
Binding sitei187 – 1871ATP1 Publication
Metal bindingi248 – 2481Magnesium or manganese 1UniRule annotation
Metal bindingi260 – 2601Magnesium or manganese 1UniRule annotation
Metal bindingi260 – 2601Magnesium or manganese 2UniRule annotation
Metal bindingi262 – 2621Magnesium or manganese 2UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi178 – 1792ATP1 Publication
Nucleotide bindingi211 – 2133ATP1 Publication

GO - Molecular functioni

  • ATP binding Source: UniProtKB-HAMAP
  • identical protein binding Source: EcoCyc
  • magnesium ion binding Source: UniProtKB-HAMAP
  • manganese ion binding Source: UniProtKB-HAMAP
  • ribosomal S6-glutamic acid ligase activity Source: EcoCyc

GO - Biological processi

  • C-terminal protein amino acid modification Source: EcoCyc
  • SOS response Source: EcoCyc
  • translation Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Ligase

Keywords - Biological processi

Protein biosynthesis

Keywords - Ligandi

ATP-binding, Magnesium, Manganese, Metal-binding, Nucleotide-binding

Enzyme and pathway databases

BioCyciEcoCyc:EG10852-MONOMER.
ECOL316407:JW0836-MONOMER.
MetaCyc:EG10852-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
Ribosomal protein S6--L-glutamate ligaseUniRule annotation (EC:6.3.2.-UniRule annotation)
Alternative name(s):
Polyglutamate synthase
Ribosomal protein S6 modification proteinUniRule annotation
Gene namesi
Name:rimK
Ordered Locus Names:b0852, JW0836
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG10852. rimK.

Pathology & Biotechi

Biotechnological usei

This protein may find application in fermentative methods that use microorganisms overexpressing rimK for mass production of poly-alpha-amino acids, which is thought to be the most economical and ecofriendly manufacturing process.1 Publication

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 300300Ribosomal protein S6--L-glutamate ligasePRO_0000205455Add
BLAST

Proteomic databases

PaxDbiP0C0U4.

Interactioni

GO - Molecular functioni

  • identical protein binding Source: EcoCyc

Protein-protein interaction databases

BioGridi4259992. 11 interactions.
IntActiP0C0U4. 4 interactions.
STRINGi511145.b0852.

Structurei

Secondary structure

1
300
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi2 – 65Combined sources
Helixi12 – 2312Combined sources
Helixi24 – 263Combined sources
Beta strandi28 – 325Combined sources
Helixi34 – 363Combined sources
Beta strandi37 – 393Combined sources
Beta strandi41 – 455Combined sources
Beta strandi48 – 503Combined sources
Beta strandi59 – 635Combined sources
Helixi70 – 8213Combined sources
Beta strandi86 – 894Combined sources
Helixi91 – 988Combined sources
Helixi100 – 10910Combined sources
Beta strandi117 – 1226Combined sources
Helixi126 – 1316Combined sources
Beta strandi136 – 1427Combined sources
Turni144 – 1474Combined sources
Beta strandi150 – 1545Combined sources
Helixi157 – 16812Combined sources
Helixi170 – 1723Combined sources
Beta strandi175 – 1795Combined sources
Beta strandi187 – 1937Combined sources
Beta strandi196 – 2049Combined sources
Beta strandi207 – 2093Combined sources
Turni214 – 2174Combined sources
Beta strandi219 – 2224Combined sources
Helixi227 – 23913Combined sources
Beta strandi243 – 25210Combined sources
Beta strandi255 – 26410Combined sources
Helixi268 – 2747Combined sources
Helixi278 – 28912Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4IWXX-ray2.85A1-300[»]
4IWYX-ray2.90A2-300[»]
ProteinModelPortaliP0C0U4.
SMRiP0C0U4. Positions 1-292.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini104 – 287184ATP-graspUniRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the RimK family.UniRule annotation
Contains 1 ATP-grasp domain.UniRule annotation

Phylogenomic databases

eggNOGiENOG4105D9I. Bacteria.
COG0189. LUCA.
HOGENOMiHOG000293092.
InParanoidiP0C0U4.
KOiK05844.
OMAiNYLRCYM.
OrthoDBiEOG6DZDX8.
PhylomeDBiP0C0U4.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
3.40.50.20. 1 hit.
HAMAPiMF_01552. RimK.
InterProiIPR011761. ATP-grasp.
IPR013651. ATP-grasp_RimK-type.
IPR013815. ATP_grasp_subdomain_1.
IPR013816. ATP_grasp_subdomain_2.
IPR016185. PreATP-grasp_dom.
IPR023533. RimK.
IPR004666. RpS6_RimK/Lys_biosynth_LsyX.
[Graphical view]
PfamiPF08443. RimK. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00768. rimK_fam. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

P0C0U4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKIAILSRDG TLYSCKRLRE AAIQRGHLVE ILDPLSCYMN INPAASSIHY
60 70 80 90 100
KGRKLPHFDA VIPRIGTAIT FYGTAALRQF EMLGSYPLNE SVAIARARDK
110 120 130 140 150
LRSMQLLARQ GIDLPVTGIA HSPDDTSDLI DMVGGAPLVV KLVEGTQGIG
160 170 180 190 200
VVLAETRQAA ESVIDAFRGL NAHILVQEYI KEAQGCDIRC LVVGDEVVAA
210 220 230 240 250
IERRAKEGDF RSNLHRGGAA SVASITPQER EIAIKAARTM ALDVAGVDIL
260 270 280 290 300
RANRGPLVME VNASPGLEGI EKTTGIDIAG KMIRWIERHA TTEYCLKTGG
Length:300
Mass (Da):32,436
Last modified:December 20, 2005 - v1
Checksum:iC0AF021292ED41DD
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti1 – 1818MKIAI…SCKRL → MERSIRVSGW in CAA33868 (PubMed:2570347).CuratedAdd
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X15859 Genomic DNA. Translation: CAA33868.1.
U00096 Genomic DNA. Translation: AAC73939.1.
AP009048 Genomic DNA. Translation: BAA35563.2.
PIRiD64823.
RefSeqiNP_415373.1. NC_000913.3.
WP_000684321.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC73939; AAC73939; b0852.
BAA35563; BAA35563; BAA35563.
GeneIDi945484.
KEGGiecj:JW0836.
eco:b0852.
PATRICi32116909. VBIEscCol129921_0880.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X15859 Genomic DNA. Translation: CAA33868.1.
U00096 Genomic DNA. Translation: AAC73939.1.
AP009048 Genomic DNA. Translation: BAA35563.2.
PIRiD64823.
RefSeqiNP_415373.1. NC_000913.3.
WP_000684321.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
4IWXX-ray2.85A1-300[»]
4IWYX-ray2.90A2-300[»]
ProteinModelPortaliP0C0U4.
SMRiP0C0U4. Positions 1-292.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4259992. 11 interactions.
IntActiP0C0U4. 4 interactions.
STRINGi511145.b0852.

Proteomic databases

PaxDbiP0C0U4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC73939; AAC73939; b0852.
BAA35563; BAA35563; BAA35563.
GeneIDi945484.
KEGGiecj:JW0836.
eco:b0852.
PATRICi32116909. VBIEscCol129921_0880.

Organism-specific databases

EchoBASEiEB0845.
EcoGeneiEG10852. rimK.

Phylogenomic databases

eggNOGiENOG4105D9I. Bacteria.
COG0189. LUCA.
HOGENOMiHOG000293092.
InParanoidiP0C0U4.
KOiK05844.
OMAiNYLRCYM.
OrthoDBiEOG6DZDX8.
PhylomeDBiP0C0U4.

Enzyme and pathway databases

BioCyciEcoCyc:EG10852-MONOMER.
ECOL316407:JW0836-MONOMER.
MetaCyc:EG10852-MONOMER.

Miscellaneous databases

PROiP0C0U4.

Family and domain databases

Gene3Di3.30.1490.20. 1 hit.
3.30.470.20. 1 hit.
3.40.50.20. 1 hit.
HAMAPiMF_01552. RimK.
InterProiIPR011761. ATP-grasp.
IPR013651. ATP-grasp_RimK-type.
IPR013815. ATP_grasp_subdomain_1.
IPR013816. ATP_grasp_subdomain_2.
IPR016185. PreATP-grasp_dom.
IPR023533. RimK.
IPR004666. RpS6_RimK/Lys_biosynth_LsyX.
[Graphical view]
PfamiPF08443. RimK. 1 hit.
[Graphical view]
TIGRFAMsiTIGR00768. rimK_fam. 1 hit.
PROSITEiPS50975. ATP_GRASP. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Characterization of the gene rimK responsible for the addition of glutamic acid residues to the C-terminus of ribosomal protein S6 in Escherichia coli K12."
    Kang W.-K., Icho T., Isono S., Kitakawa M., Isono K.
    Mol. Gen. Genet. 217:281-288(1989) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], IDENTIFICATION, FUNCTION.
    Strain: K12.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / MG1655 / ATCC 47076.
  4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
    Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
    Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
  5. "Poly-alpha-glutamic acid synthesis using a novel catalytic activity of RimK from Escherichia coli K-12."
    Kino K., Arai T., Arimura Y.
    Appl. Environ. Microbiol. 77:2019-2025(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, BIOTECHNOLOGY.
    Strain: K12.
  6. "Structure and function of Escherichia coli RimK, an ATP-grasp fold, L-glutamyl ligase enzyme."
    Zhao G., Jin Z., Wang Y., Allewell N.M., Tuchman M., Shi D.
    Proteins 81:1847-1854(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS) IN COMPLEX WITH ADP, SUBUNIT.

Entry informationi

Entry nameiRIMK_ECOLI
AccessioniPrimary (citable) accession number: P0C0U4
Secondary accession number(s): P17116, P75814
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: December 20, 2005
Last modified: January 20, 2016
This is version 90 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.