CBIA_METM5
ID CBIA_METM5 Reviewed; 447 AA.
AC A4FW46;
DT 20-MAY-2008, integrated into UniProtKB/Swiss-Prot.
DT 17-APR-2007, sequence version 1.
DT 25-MAY-2022, entry version 86.
DE RecName: Full=Cobyrinate a,c-diamide synthase {ECO:0000255|HAMAP-Rule:MF_00027};
DE EC=6.3.5.11 {ECO:0000255|HAMAP-Rule:MF_00027};
DE AltName: Full=Cobyrinic acid a,c-diamide synthetase {ECO:0000255|HAMAP-Rule:MF_00027};
DE AltName: Full=Ni-sirohydrochlorin a,c-diamide synthase {ECO:0000255|HAMAP-Rule:MF_00027};
DE EC=6.3.5.12 {ECO:0000255|HAMAP-Rule:MF_00027};
DE AltName: Full=Ni-sirohydrochlorin a,c-diamide synthetase {ECO:0000255|HAMAP-Rule:MF_00027};
GN Name=cbiA {ECO:0000255|HAMAP-Rule:MF_00027};
GN Synonyms=cfbB {ECO:0000255|HAMAP-Rule:MF_00027};
GN OrderedLocusNames=MmarC5_0100;
OS Methanococcus maripaludis (strain C5 / ATCC BAA-1333).
OC Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC Methanococcaceae; Methanococcus.
OX NCBI_TaxID=402880;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C5 / ATCC BAA-1333;
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Glavina del Rio T., Dalin E.,
RA Tice H., Pitluck S., Chertkov O., Brettin T., Bruce D., Han C.,
RA Detter J.C., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N.,
RA Mikhailova N., Sieprawska-Lupa M., Whitman W.B., Richardson P.;
RT "Complete sequence of chromosome of Methanococcus maripaludis C5.";
RL Submitted (MAR-2007) 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:0000255|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:0000255|HAMAP-
CC 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:0000255|HAMAP-Rule:MF_00027};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|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:0000255|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:0000255|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:0000255|HAMAP-Rule:MF_00027}.
CC -!- SIMILARITY: Belongs to the CobB/CbiA family. {ECO:0000255|HAMAP-
CC Rule:MF_00027}.
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DR EMBL; CP000609; ABO34417.1; -; Genomic_DNA.
DR RefSeq; WP_011867878.1; NC_009135.1.
DR AlphaFoldDB; A4FW46; -.
DR SMR; A4FW46; -.
DR STRING; 402880.MmarC5_0100; -.
DR EnsemblBacteria; ABO34417; ABO34417; MmarC5_0100.
DR GeneID; 4927520; -.
DR KEGG; mmq:MmarC5_0100; -.
DR eggNOG; arCOG00106; Archaea.
DR HOGENOM; CLU_022752_2_0_2; -.
DR OMA; MYLTNSI; -.
DR OrthoDB; 14023at2157; -.
DR UniPathway; UPA00148; UER00231.
DR Proteomes; UP000000253; 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-KW.
DR GO; GO:0015948; P:methanogenesis; IEA:UniProtKB-KW.
DR Gene3D; 3.40.50.300; -; 1.
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; 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;
KW ATP-binding; Cobalamin biosynthesis; Glutamine amidotransferase; Ligase;
KW Magnesium; Methanogenesis; Nucleotide-binding.
FT CHAIN 1..447
FT /note="Cobyrinate a,c-diamide synthase"
FT /id="PRO_1000074390"
FT DOMAIN 252..439
FT /note="GATase cobBQ-type"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00027"
FT ACT_SITE 331
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00027"
FT SITE 431
FT /note="Increases nucleophilicity of active site Cys"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00027"
SQ SEQUENCE 447 AA; 50199 MW; 9C238529B7F8F076 CRC64;
MKRVVIAGTS SMVGKTTIST GIMKALSKKN NVQPYKIGPD YIDPTYHTEA TKNKSRNLDS
FFMDEMQVRS IFKRHSKNKD INVIEGVRGL YEGISPYNDV GSTASVSKTL NAPVILLMDA
RSLTRSAAAI IKGFKSFDTE LNIKGVIFNK IRGEGHLNKL KEAVKYYDND IEIIGAIPRD
DGLSVSQRHL GLVPTPENKQ KLLERIDLWG NTVEECLDIE KIVELSDESF DFEVDEKNKE
ETLWKVEKNN SKIAVAFDES FNFYYWDNFD ALEENGAKIK FFSPLNDVEV PDCDTIYLGG
GYPELFSEKL SNNKSMIDSI RNFDGKIYGE CGGLMYLTNS IDGKEMLKLI DADAVMTPNV
QGLSYVKGTF EKDCIIGEKS KEFKAHEFHY SKLININEND FSYRINRGKG IINSMDGITS
KDGDIVGGYA HQHCIGNPYF AANLSKT
