ID Q0W386_METAR Unreviewed; 464 AA.
AC Q0W386;
DT 05-SEP-2006, integrated into UniProtKB/TrEMBL.
DT 05-SEP-2006, sequence version 1.
DT 27-MAR-2024, entry version 109.
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-1 {ECO:0000313|EMBL:CAJ37157.1};
GN Synonyms=cbiA {ECO:0000256|HAMAP-Rule:MF_00027}, cfbB
GN {ECO:0000256|HAMAP-Rule:MF_00027};
GN ORFNames=RCIX2001 {ECO:0000313|EMBL:CAJ37157.1};
OS Methanocella arvoryzae (strain DSM 22066 / NBRC 105507 / MRE50).
OC Archaea; Euryarchaeota; Stenosarchaea group; Methanomicrobia;
OC Methanocellales; Methanocellaceae; Methanocella.
OX NCBI_TaxID=351160 {ECO:0000313|EMBL:CAJ37157.1, ECO:0000313|Proteomes:UP000000663};
RN [1] {ECO:0000313|EMBL:CAJ37157.1, ECO:0000313|Proteomes:UP000000663}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 22066 / NBRC 105507 / MRE50
RC {ECO:0000313|Proteomes:UP000000663};
RX PubMed=16857943; DOI=10.1126/science.1127062;
RA Erkel C., Kube M., Reinhardt R., Liesack W.;
RT "Genome of rice cluster I archaea -- the key methane producers in the rice
RT rhizosphere.";
RL Science 313:370-372(2006).
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|ARBA:ARBA00001946,
CC 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; AM114193; CAJ37157.1; -; Genomic_DNA.
DR RefSeq; WP_012035417.1; NC_009464.1.
DR AlphaFoldDB; Q0W386; -.
DR STRING; 351160.RCIX2001; -.
DR GeneID; 5145274; -.
DR KEGG; rci:RCIX2001; -.
DR PATRIC; fig|351160.9.peg.1125; -.
DR eggNOG; arCOG00106; Archaea.
DR OrthoDB; 8896at2157; -.
DR UniPathway; UPA00148; UER00231.
DR Proteomes; UP000000663; Chromosome.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
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 CDD; cd05388; CobB_N; 1.
DR CDD; cd03130; GATase1_CobB; 1.
DR Gene3D; 3.40.50.880; -; 1.
DR Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 1.
DR HAMAP; MF_00027; CobB_CbiA; 1.
DR InterPro; IPR004484; CbiA/CobB_synth.
DR InterPro; IPR029062; Class_I_gatase-like.
DR InterPro; IPR002586; CobQ/CobB/MinD/ParA_Nub-bd_dom.
DR InterPro; IPR011698; GATase_3.
DR InterPro; IPR027417; P-loop_NTPase.
DR NCBIfam; TIGR00379; cobB; 1.
DR NCBIfam; NF033195; F430_CfbB; 1.
DR PANTHER; PTHR43873; COBYRINATE A,C-DIAMIDE SYNTHASE; 1.
DR PANTHER; PTHR43873:SF1; COBYRINATE A,C-DIAMIDE SYNTHASE; 1.
DR Pfam; PF01656; CbiA; 1.
DR Pfam; PF07685; GATase_3; 1.
DR SUPFAM; SSF52317; Class I glutamine amidotransferase-like; 1.
DR SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 1.
DR PROSITE; PS51274; GATASE_COBBQ; 1.
PE 3: Inferred from homology;
KW ATP-binding {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|HAMAP-
KW Rule:MF_00027}; Cobalamin biosynthesis {ECO:0000256|HAMAP-Rule:MF_00027};
KW Glutamine amidotransferase {ECO:0000256|ARBA:ARBA00022962,
KW ECO:0000256|HAMAP-Rule:MF_00027};
KW Ligase {ECO:0000256|ARBA:ARBA00022598, ECO:0000256|HAMAP-Rule:MF_00027};
KW Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|HAMAP-Rule:MF_00027};
KW Methanogenesis {ECO:0000256|HAMAP-Rule:MF_00027};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|HAMAP-
KW Rule:MF_00027}; Reference proteome {ECO:0000313|Proteomes:UP000000663}.
FT DOMAIN 8..192
FT /note="CobQ/CobB/MinD/ParA nucleotide binding"
FT /evidence="ECO:0000259|Pfam:PF01656"
FT DOMAIN 255..445
FT /note="CobB/CobQ-like glutamine amidotransferase"
FT /evidence="ECO:0000259|Pfam:PF07685"
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 464 AA; 50377 MW; F11276F2FD9FB6EE CRC64;
MIKIPRVILA GDRSSAGKTT ISVGIMALLK EQGKTVQPFK VGLDYIDPSY HSMITGKQGG
NLDGYLMSDK AIAEAFVHSS EGSDISIIEG VRGLYEGLES LSDVGSTAQI AKVLKTPVIL
IVDAQSITRS TAAIVKGYRD FDRGVNIRGV ILNKIGSERH AEKARMAIEK YTGVEVLGAI
PRSNSMKLTM RHLGLIPARE GASRVEGFDS KLEKIKETIR DNLNLKRIVE IAAGAPPLRE
PKPDIFVRKN PGGVRIGLAL DEAFNFYYKD NIDLLQCRGA EIVHFSPVND AGIPEVDGLI
IGGGYPEVFA AELAQNEAMR KSIFEASRRG MPIYAECGGL MYLMKSLETE DGSRHDMAGV
FEGVASMKHV RTIGYVSGRF AMDTPIGQEG ALFKGHEFHH SVITDLASNA RFACRLDRGT
GIHNGLDGIM SDNTLATYTH LHAASYVPFS GKFVESCAVY HEKG
//
