(data stored in SCRATCH zone)

SWISSPROT: D1YVG5_METPS

ID   D1YVG5_METPS            Unreviewed;       463 AA.
AC   D1YVG5;
DT   09-FEB-2010, integrated into UniProtKB/TrEMBL.
DT   09-FEB-2010, sequence version 1.
DT   11-DEC-2019, entry version 60.
DE   RecName: Full=Cobyrinate a,c-diamide synthase {ECO:0000256|HAMAP-Rule:MF_00027};
DE            EC=6.3.5.11 {ECO:0000256|HAMAP-Rule:MF_00027};
DE   AltName: Full=Cobyrinic acid a,c-diamide synthetase {ECO:0000256|HAMAP-Rule:MF_00027};
DE   AltName: Full=Ni-sirohydrochlorin a,c-diamide synthase {ECO:0000256|HAMAP-Rule:MF_00027};
DE            EC=6.3.5.12 {ECO:0000256|HAMAP-Rule:MF_00027};
DE   AltName: Full=Ni-sirohydrochlorin a,c-diamide synthetase {ECO:0000256|HAMAP-Rule:MF_00027};
GN   Name=cbiA {ECO:0000256|HAMAP-Rule:MF_00027};
GN   Synonyms=cfbB {ECO:0000256|HAMAP-Rule:MF_00027}, cobB
GN   {ECO:0000313|EMBL:BAI60437.1};
GN   OrderedLocusNames=MCP_0365 {ECO:0000313|EMBL:BAI60437.1};
OS   Methanocella paludicola (strain DSM 17711 / JCM 13418 / NBRC 101707 /
OS   SANAE).
OC   Archaea; Euryarchaeota; Stenosarchaea group; Methanomicrobia;
OC   Methanocellales; Methanocellaceae; Methanocella.
OX   NCBI_TaxID=304371 {ECO:0000313|EMBL:BAI60437.1, ECO:0000313|Proteomes:UP000001882};
RN   [1] {ECO:0000313|Proteomes:UP000001882}
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 17711 / JCM 13418 / NBRC 101707 / SANAE
RC   {ECO:0000313|Proteomes:UP000001882};
RX   PubMed=21829548; DOI=10.1371/journal.pone.0022898;
RA   Sakai S., Takaki Y., Shimamura S., Sekine M., Tajima T., Kosugi H.,
RA   Ichikawa N., Tasumi E., Hiraki A.T., Shimizu A., Kato Y., Nishiko R.,
RA   Mori K., Fujita N., Imachi H., Takai K.;
RT   "Genome sequence of a mesophilic hydrogenotrophic methanogen Methanocella
RT   paludicola, the first cultivated representative of the order
RT   Methanocellales.";
RL   PLoS ONE 6:E22898-E22898(2011).
CC   -!- FUNCTION: Catalyzes the ATP-dependent amidation of the two carboxylate
CC       groups at positions a and c of cobyrinate, using either L-glutamine or
CC       ammonia as the nitrogen source. Involved in the biosynthesis of the
CC       unique nickel-containing tetrapyrrole coenzyme F430, the prosthetic
CC       group of methyl-coenzyme M reductase (MCR), which plays a key role in
CC       methanogenesis and anaerobic methane oxidation. Catalyzes the ATP-
CC       dependent amidation of the two carboxylate groups at positions a and c
CC       of Ni-sirohydrochlorin, using L-glutamine or ammonia as the nitrogen
CC       source. {ECO:0000256|HAMAP-Rule:MF_00027}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=2 ATP + 2 H2O + 2 L-glutamine + Ni-sirohydrochlorin = 2 ADP +
CC         2 H(+) + 2 L-glutamate + Ni-sirohydrochlorin a,c-diamide + 2
CC         phosphate; Xref=Rhea:RHEA:52896, ChEBI:CHEBI:15377,
CC         ChEBI:CHEBI:15378, ChEBI:CHEBI:29985, ChEBI:CHEBI:30616,
CC         ChEBI:CHEBI:43474, ChEBI:CHEBI:58359, ChEBI:CHEBI:136841,
CC         ChEBI:CHEBI:136887, ChEBI:CHEBI:456216; EC=6.3.5.12;
CC         Evidence={ECO:0000256|HAMAP-Rule:MF_00027};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=2 ATP + cob(II)yrinate + 2 H2O + 2 L-glutamine = 2 ADP +
CC         cob(II)yrinate a,c diamide + 2 H(+) + 2 L-glutamate + 2 phosphate;
CC         Xref=Rhea:RHEA:26289, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC         ChEBI:CHEBI:29985, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474,
CC         ChEBI:CHEBI:58359, ChEBI:CHEBI:58537, ChEBI:CHEBI:58894,
CC         ChEBI:CHEBI:456216; EC=6.3.5.11; Evidence={ECO:0000256|HAMAP-
CC         Rule:MF_00027};
CC   -!- COFACTOR:
CC       Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC         Evidence={ECO:0000256|HAMAP-Rule:MF_00027};
CC   -!- PATHWAY: Cofactor biosynthesis; adenosylcobalamin biosynthesis;
CC       cob(II)yrinate a,c-diamide from sirohydrochlorin (anaerobic route):
CC       step 10/10. {ECO:0000256|HAMAP-Rule:MF_00027}.
CC   -!- DOMAIN: Comprises of two domains. The C-terminal domain contains the
CC       binding site for glutamine and catalyzes the hydrolysis of this
CC       substrate to glutamate and ammonia. The N-terminal domain is
CC       anticipated to bind ATP, and cobyrinate or Ni-sirohydrochlorin, and
CC       catalyzes the ultimate synthesis of the diamide product. The ammonia
CC       produced via the glutaminase domain is probably translocated to the
CC       adjacent domain via a molecular tunnel, where it reacts with an
CC       activated intermediate. {ECO:0000256|HAMAP-Rule:MF_00027}.
CC   -!- MISCELLANEOUS: The a and c carboxylates of cobyrinate and Ni-
CC       sirohydrochlorin are activated for nucleophilic attack via formation of
CC       a phosphorylated intermediate by ATP. CbiA catalyzes first the
CC       amidation of the c-carboxylate, and then that of the a-carboxylate.
CC       {ECO:0000256|HAMAP-Rule:MF_00027}.
CC   -!- SIMILARITY: Belongs to the CobB/CbiA family. {ECO:0000256|HAMAP-
CC       Rule:MF_00027}.
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DR   EMBL; AP011532; BAI60437.1; -; Genomic_DNA.
DR   STRING; 304371.MCP_0365; -.
DR   EnsemblBacteria; BAI60437; BAI60437; MCP_0365.
DR   KEGG; mpd:MCP_0365; -.
DR   PATRIC; fig|304371.9.peg.374; -.
DR   eggNOG; arCOG00106; Archaea.
DR   eggNOG; COG1797; LUCA.
DR   HOGENOM; HOG000289958; -.
DR   KO; K22012; -.
DR   OMA; MYLTNSI; -.
DR   UniPathway; UPA00148; UER00231.
DR   Proteomes; UP000001882; Chromosome.
DR   GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR   GO; GO:0043775; F:cobyrinate a,c-diamide synthase activity; IEA:UniProtKB-EC.
DR   GO; GO:0042242; F:cobyrinic acid a,c-diamide synthase activity; IEA:UniProtKB-UniRule.
DR   GO; GO:0009236; P:cobalamin biosynthetic process; IEA:UniProtKB-UniRule.
DR   GO; GO:0006541; P:glutamine metabolic process; IEA:UniProtKB-UniRule.
DR   GO; GO:0015948; P:methanogenesis; IEA:UniProtKB-KW.
DR   Gene3D; 3.40.50.880; -; 1.
DR   HAMAP; MF_00027; CobB_CbiA; 1.
DR   InterPro; IPR004484; CbiA_synth.
DR   InterPro; IPR029062; Class_I_gatase-like.
DR   InterPro; IPR017929; CobB/CobQ_GATase.
DR   InterPro; IPR002586; CobQ/CobB/MinD/ParA_Nub-bd_dom.
DR   InterPro; IPR011698; GATase_3.
DR   InterPro; IPR027417; P-loop_NTPase.
DR   PANTHER; PTHR43873; PTHR43873; 1.
DR   Pfam; PF01656; CbiA; 1.
DR   Pfam; PF07685; GATase_3; 1.
DR   SUPFAM; SSF52317; SSF52317; 1.
DR   SUPFAM; SSF52540; SSF52540; 1.
DR   TIGRFAMs; TIGR00379; cobB; 1.
DR   PROSITE; PS51274; GATASE_COBBQ; 1.
PE   3: Inferred from homology;
DR   PRODOM; D1YVG5.
DR   SWISS-2DPAGE; D1YVG5.
KW   ATP-binding {ECO:0000256|HAMAP-Rule:MF_00027};
KW   Cobalamin biosynthesis {ECO:0000256|HAMAP-Rule:MF_00027};
KW   Glutamine amidotransferase {ECO:0000256|HAMAP-Rule:MF_00027,
KW   ECO:0000256|PROSITE-ProRule:PRU00606};
KW   Ligase {ECO:0000256|HAMAP-Rule:MF_00027};
KW   Magnesium {ECO:0000256|HAMAP-Rule:MF_00027};
KW   Methanogenesis {ECO:0000256|HAMAP-Rule:MF_00027};
KW   Nucleotide-binding {ECO:0000256|HAMAP-Rule:MF_00027};
KW   Reference proteome {ECO:0000313|Proteomes:UP000001882}.
FT   DOMAIN          255..448
FT                   /note="GATase cobBQ-type"
FT                   /evidence="ECO:0000259|PROSITE:PS51274"
FT   ACT_SITE        337
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
FT   SITE            440
FT                   /note="Increases nucleophilicity of active site Cys"
FT                   /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
SQ   SEQUENCE   463 AA;  50305 MW;  BF69ECF1531671B2 CRC64;
     MMTMPRLILA GDRSSAGKTT ISTGVMSLLH ERGMKVQPFK VGLDYIDPSY HSLATGRQGE
     NLDGYLMSEQ AIVEAFQHSA GGSDIAIIEG VRGLYEGLEA LSDIGSTAQI AKILKTPVVL
     VLDAQSITRS TAAIVKGYKD FDKGINFKGV ILNKVGSDRH AEKATAAIQK YTGVEVLGAI
     PRNKGMSLTM RHLGLVPARE GASRVDDFDA RITKIKEIIG EHVNLDRLLE IANGAPKLRT
     GKQSIFKQEK SAGVRIGVAL DEAFNFYYKD NVDLLQLKGA EVVYFSPLHD REIPDVDGLI
     IGGGYPEFFA RELSDNGSMR KSIADASVNG MPIYAECGGM MYLTSALEDE HGKKFDMVGV
     MGGVASMKHI RHIGYVAGQL EKDTPIGEKG TFFKGHEFHY SVITDVPFDA KFAYRMDRGT
     GIKDGLDGML TNNTLGSYTH LHAASYVPFA RSFVDACVEH KGP
//

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