RIMK_ECOLI
ID RIMK_ECOLI Reviewed; 300 AA.
AC P0C0U4; P17116; P75814;
DT 20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 20-DEC-2005, sequence version 1.
DT 03-AUG-2022, entry version 123.
DE RecName: Full=Ribosomal protein S6--L-glutamate ligase {ECO:0000255|HAMAP-Rule:MF_01552};
DE EC=6.3.2.- {ECO:0000255|HAMAP-Rule:MF_01552};
DE AltName: Full=Polyglutamate synthase;
DE AltName: Full=Ribosomal protein S6 modification protein {ECO:0000255|HAMAP-Rule:MF_01552};
GN Name=rimK; OrderedLocusNames=b0852, JW0836;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], IDENTIFICATION, AND FUNCTION.
RC STRAIN=K12;
RX PubMed=2570347; DOI=10.1007/bf02464894;
RA Kang W.-K., Icho T., Isono S., Kitakawa M., Isono K.;
RT "Characterization of the gene rimK responsible for the addition of glutamic
RT acid residues to the C-terminus of ribosomal protein S6 in Escherichia coli
RT K12.";
RL Mol. Gen. Genet. 217:281-288(1989).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=8905232; DOI=10.1093/dnares/3.3.137;
RA Oshima T., Aiba H., Baba T., Fujita K., Hayashi K., Honjo A., Ikemoto K.,
RA Inada T., Itoh T., Kajihara M., Kanai K., Kashimoto K., Kimura S.,
RA Kitagawa M., Makino K., Masuda S., Miki T., Mizobuchi K., Mori H.,
RA Motomura K., Nakamura Y., Nashimoto H., Nishio Y., Saito N., Sampei G.,
RA Seki Y., Tagami H., Takemoto K., Wada C., Yamamoto Y., Yano M.,
RA Horiuchi T.;
RT "A 718-kb DNA sequence of the Escherichia coli K-12 genome corresponding to
RT the 12.7-28.0 min region on the linkage map.";
RL DNA Res. 3:137-155(1996).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT, AND
RP BIOTECHNOLOGY.
RC STRAIN=K12;
RX PubMed=21278279; DOI=10.1128/aem.02043-10;
RA Kino K., Arai T., Arimura Y.;
RT "Poly-alpha-glutamic acid synthesis using a novel catalytic activity of
RT RimK from Escherichia coli K-12.";
RL Appl. Environ. Microbiol. 77:2019-2025(2011).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (2.85 ANGSTROMS) IN COMPLEX WITH ADP, AND SUBUNIT.
RX PubMed=23609986; DOI=10.1002/prot.24311;
RA Zhao G., Jin Z., Wang Y., Allewell N.M., Tuchman M., Shi D.;
RT "Structure and function of Escherichia coli RimK, an ATP-grasp fold, L-
RT glutamyl ligase enzyme.";
RL Proteins 81:1847-1854(2013).
CC -!- FUNCTION: Is an L-glutamate ligase that catalyzes the ATP-dependent
CC post-translational addition of glutamate residues to the C-terminus of
CC ribosomal protein S6 (RpsF). Is also able to catalyze the synthesis of
CC poly-alpha-glutamate in vitro, via ATP hydrolysis from unprotected
CC glutamate as substrate. The number of glutamate residues added to
CC either RpsF or to poly-alpha-glutamate changes with pH.
CC {ECO:0000255|HAMAP-Rule:MF_01552, ECO:0000269|PubMed:21278279,
CC ECO:0000269|PubMed:2570347}.
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01552};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01552};
CC Note=Binds 2 magnesium or manganese ions per subunit.
CC {ECO:0000255|HAMAP-Rule:MF_01552};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 9.5 for RpsF modification and 9 for polyglutamate
CC synthase activity. {ECO:0000269|PubMed:21278279};
CC Temperature dependence:
CC Shows thermal stability. Exhibits 86% activity after incubation at 55
CC degrees Celsius for 15 minutes, but its activity decreases sharply at
CC 60 degrees Celsius. {ECO:0000269|PubMed:21278279};
CC -!- BIOTECHNOLOGY: This protein may find application in fermentative
CC methods that use microorganisms overexpressing rimK for mass production
CC of poly-alpha-amino acids, which is thought to be the most economical
CC and ecofriendly manufacturing process. {ECO:0000269|PubMed:21278279}.
CC -!- SIMILARITY: Belongs to the RimK family. {ECO:0000255|HAMAP-
CC Rule:MF_01552}.
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DR EMBL; X15859; CAA33868.1; -; Genomic_DNA.
DR EMBL; U00096; AAC73939.1; -; Genomic_DNA.
DR EMBL; AP009048; BAA35563.2; -; Genomic_DNA.
DR PIR; D64823; D64823.
DR RefSeq; NP_415373.1; NC_000913.3.
DR RefSeq; WP_000684321.1; NZ_STEB01000019.1.
DR PDB; 4IWX; X-ray; 2.85 A; A=1-300.
DR PDB; 4IWY; X-ray; 2.90 A; A=2-300.
DR PDB; 5ZCT; X-ray; 2.05 A; A/B/C/D/E/F/G/H=1-292.
DR PDB; 5ZK6; X-ray; 3.15 A; A=1-300.
DR PDBsum; 4IWX; -.
DR PDBsum; 4IWY; -.
DR PDBsum; 5ZCT; -.
DR PDBsum; 5ZK6; -.
DR AlphaFoldDB; P0C0U4; -.
DR SMR; P0C0U4; -.
DR BioGRID; 4259992; 31.
DR IntAct; P0C0U4; 4.
DR STRING; 511145.b0852; -.
DR jPOST; P0C0U4; -.
DR PaxDb; P0C0U4; -.
DR PRIDE; P0C0U4; -.
DR EnsemblBacteria; AAC73939; AAC73939; b0852.
DR EnsemblBacteria; BAA35563; BAA35563; BAA35563.
DR GeneID; 58460667; -.
DR GeneID; 945484; -.
DR KEGG; ecj:JW0836; -.
DR KEGG; eco:b0852; -.
DR PATRIC; fig|1411691.4.peg.1426; -.
DR EchoBASE; EB0845; -.
DR eggNOG; COG0189; Bacteria.
DR HOGENOM; CLU_054353_0_1_6; -.
DR InParanoid; P0C0U4; -.
DR OMA; CYMNIAS; -.
DR PhylomeDB; P0C0U4; -.
DR BioCyc; EcoCyc:EG10852-MON; -.
DR BioCyc; MetaCyc:EG10852-MON; -.
DR PRO; PR:P0C0U4; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0042802; F:identical protein binding; IDA:EcoCyc.
DR GO; GO:0016879; F:ligase activity, forming carbon-nitrogen bonds; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0018169; F:ribosomal S6-glutamic acid ligase activity; IDA:EcoCyc.
DR GO; GO:0018410; P:C-terminal protein amino acid modification; IMP:EcoCyc.
DR GO; GO:0009432; P:SOS response; IMP:EcoCyc.
DR GO; GO:0006412; P:translation; IEA:UniProtKB-KW.
DR Gene3D; 3.30.1490.20; -; 1.
DR HAMAP; MF_01552; RimK; 1.
DR InterPro; IPR011761; ATP-grasp.
DR InterPro; IPR013651; ATP-grasp_RimK-type.
DR InterPro; IPR013815; ATP_grasp_subdomain_1.
DR InterPro; IPR023533; RimK.
DR InterPro; IPR041107; Rimk_N.
DR InterPro; IPR004666; RpS6_RimK/Lys_biosynth_LsyX.
DR Pfam; PF08443; RimK; 1.
DR Pfam; PF18030; Rimk_N; 1.
DR TIGRFAMs; TIGR00768; rimK_fam; 1.
DR PROSITE; PS50975; ATP_GRASP; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Ligase; Magnesium; Manganese; Metal-binding;
KW Nucleotide-binding; Protein biosynthesis; Reference proteome.
FT CHAIN 1..300
FT /note="Ribosomal protein S6--L-glutamate ligase"
FT /id="PRO_0000205455"
FT DOMAIN 104..287
FT /note="ATP-grasp"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01552"
FT BINDING 141
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|PubMed:23609986"
FT BINDING 178..179
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|PubMed:23609986"
FT BINDING 187
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|PubMed:23609986"
FT BINDING 211..213
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000305|PubMed:23609986"
FT BINDING 248
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01552"
FT BINDING 248
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01552"
FT BINDING 260
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01552"
FT BINDING 260
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01552"
FT BINDING 260
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01552"
FT BINDING 260
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01552"
FT BINDING 262
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01552"
FT BINDING 262
FT /ligand="Mn(2+)"
FT /ligand_id="ChEBI:CHEBI:29035"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01552"
FT CONFLICT 1..18
FT /note="MKIAILSRDGTLYSCKRL -> MERSIRVSGW (in Ref. 1;
FT CAA33868)"
FT /evidence="ECO:0000305"
FT STRAND 2..8
FT /evidence="ECO:0007829|PDB:5ZCT"
FT STRAND 10..12
FT /evidence="ECO:0007829|PDB:5ZK6"
FT HELIX 13..24
FT /evidence="ECO:0007829|PDB:5ZCT"
FT STRAND 28..32
FT /evidence="ECO:0007829|PDB:5ZCT"
FT HELIX 34..36
FT /evidence="ECO:0007829|PDB:5ZCT"
FT STRAND 37..43
FT /evidence="ECO:0007829|PDB:5ZCT"
FT STRAND 48..50
FT /evidence="ECO:0007829|PDB:5ZCT"
FT STRAND 59..64
FT /evidence="ECO:0007829|PDB:5ZCT"
FT HELIX 67..69
FT /evidence="ECO:0007829|PDB:5ZCT"
FT HELIX 70..82
FT /evidence="ECO:0007829|PDB:5ZCT"
FT STRAND 86..89
FT /evidence="ECO:0007829|PDB:5ZCT"
FT HELIX 91..98
FT /evidence="ECO:0007829|PDB:5ZCT"
FT HELIX 100..109
FT /evidence="ECO:0007829|PDB:5ZCT"
FT STRAND 117..122
FT /evidence="ECO:0007829|PDB:5ZCT"
FT HELIX 126..133
FT /evidence="ECO:0007829|PDB:5ZCT"
FT STRAND 135..142
FT /evidence="ECO:0007829|PDB:5ZCT"
FT TURN 147..150
FT /evidence="ECO:0007829|PDB:5ZCT"
FT STRAND 151..154
FT /evidence="ECO:0007829|PDB:5ZCT"
FT HELIX 157..168
FT /evidence="ECO:0007829|PDB:5ZCT"
FT HELIX 170..172
FT /evidence="ECO:0007829|PDB:4IWX"
FT STRAND 174..178
FT /evidence="ECO:0007829|PDB:5ZCT"
FT HELIX 181..183
FT /evidence="ECO:0007829|PDB:5ZCT"
FT STRAND 186..193
FT /evidence="ECO:0007829|PDB:5ZCT"
FT STRAND 196..204
FT /evidence="ECO:0007829|PDB:5ZCT"
FT STRAND 207..209
FT /evidence="ECO:0007829|PDB:4IWX"
FT HELIX 214..216
FT /evidence="ECO:0007829|PDB:5ZCT"
FT STRAND 219..222
FT /evidence="ECO:0007829|PDB:5ZCT"
FT HELIX 227..239
FT /evidence="ECO:0007829|PDB:5ZCT"
FT STRAND 243..252
FT /evidence="ECO:0007829|PDB:5ZCT"
FT STRAND 255..264
FT /evidence="ECO:0007829|PDB:5ZCT"
FT HELIX 268..274
FT /evidence="ECO:0007829|PDB:5ZCT"
FT HELIX 278..289
FT /evidence="ECO:0007829|PDB:5ZCT"
SQ SEQUENCE 300 AA; 32436 MW; C0AF021292ED41DD CRC64;
MKIAILSRDG TLYSCKRLRE AAIQRGHLVE ILDPLSCYMN INPAASSIHY KGRKLPHFDA
VIPRIGTAIT FYGTAALRQF EMLGSYPLNE SVAIARARDK LRSMQLLARQ GIDLPVTGIA
HSPDDTSDLI DMVGGAPLVV KLVEGTQGIG VVLAETRQAA ESVIDAFRGL NAHILVQEYI
KEAQGCDIRC LVVGDEVVAA IERRAKEGDF RSNLHRGGAA SVASITPQER EIAIKAARTM
ALDVAGVDIL RANRGPLVME VNASPGLEGI EKTTGIDIAG KMIRWIERHA TTEYCLKTGG
