ID A0A0Q1AS86_9EURY Unreviewed; 441 AA.
AC A0A0Q1AS86;
DT 20-JAN-2016, integrated into UniProtKB/TrEMBL.
DT 20-JAN-2016, sequence version 1.
DT 27-MAR-2024, entry version 35.
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};
GN ORFNames=APR55_00965 {ECO:0000313|EMBL:KQC07361.1};
OS Methanolinea sp. SDB.
OC Archaea; Euryarchaeota; Stenosarchaea group; Methanomicrobia;
OC Methanomicrobiales; Methanoregulaceae; Methanolinea.
OX NCBI_TaxID=1735327 {ECO:0000313|EMBL:KQC07361.1, ECO:0000313|Proteomes:UP000050878};
RN [1] {ECO:0000313|EMBL:KQC07361.1, ECO:0000313|Proteomes:UP000050878}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=SDB {ECO:0000313|EMBL:KQC07361.1};
RA Wawrik B., Marks C.R., Davidova I.A., Mcinerney M.J., Pruitt S., Duncan K.,
RA Suflita J.M., Callaghan A.V.;
RT "Metagenomic Analysis of a Methanogenic Paraffin-Utilizing Consortium.";
RL Submitted (OCT-2015) to the EMBL/GenBank/DDBJ databases.
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}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:KQC07361.1}.
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DR EMBL; LKUF01000283; KQC07361.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A0Q1AS86; -.
DR UniPathway; UPA00148; UER00231.
DR Proteomes; UP000050878; Unassembled WGS sequence.
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; 2.
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 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}.
FT DOMAIN 7..167
FT /note="CobQ/CobB/MinD/ParA nucleotide binding"
FT /evidence="ECO:0000259|Pfam:PF01656"
FT DOMAIN 239..424
FT /note="CobB/CobQ-like glutamine amidotransferase"
FT /evidence="ECO:0000259|Pfam:PF07685"
FT ACT_SITE 319
FT /note="Nucleophile"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
FT SITE 420
FT /note="Increases nucleophilicity of active site Cys"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
SQ SEQUENCE 441 AA; 47680 MW; F986D0AF3A29E375 CRC64;
MPHIPRIVIA GTHSGCGKTT IARGIMDALT RRGLRVQPFK VGPDFIDPTH HTVICGRSSR
NLDPFMMGGD GVLETFVRAS QGRDIAVIEG VMGMYDGLMG SDHASTAHVM RILQAPAALV
VDVRGMSRSA NAVVRGFCDF GDGEEIAGVI YNRVGSPRHR AMIEESLVTR PFGFVPVDRE
CTIESRHLGL RMAHELEKSQ CIGDLIENSC DLDAMLDAAR AVPVLPDIPD RQAMPESVRI
GVADDEAFCF YYQDNLDSLA RAGAEIILFS PIHDPFPEID ALYLGGGYPE LHAAGLERSA
FGEAARKAAD DGMPIYAECG GLLALSESIE TDREYAMAGI LPARARMTGR IQALGYSDGE
WTGGLSFARP GSRILGHEFH YSCVECKADA RFSIRLARGS GISEGLDGLY VHQAAGTYMH
AYFSPEFARA FVSSAAAYKK S
//
