ID F0T7A6_METLA Unreviewed; 451 AA.
AC F0T7A6;
DT 03-MAY-2011, integrated into UniProtKB/TrEMBL.
DT 03-MAY-2011, sequence version 1.
DT 27-MAR-2024, entry version 70.
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 OrderedLocusNames=Metbo_0082 {ECO:0000313|EMBL:ADZ08335.1};
OS Methanobacterium lacus (strain AL-21).
OC Archaea; Euryarchaeota; Methanomada group; Methanobacteria;
OC Methanobacteriales; Methanobacteriaceae; Methanobacterium.
OX NCBI_TaxID=877455 {ECO:0000313|EMBL:ADZ08335.1, ECO:0000313|Proteomes:UP000007490};
RN [1] {ECO:0000313|Proteomes:UP000007490}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AL-21 {ECO:0000313|Proteomes:UP000007490};
RG US DOE Joint Genome Institute;
RA Lucas S., Copeland A., Lapidus A., Cheng J.-F., Goodwin L., Pitluck S.,
RA Chertkov O., Detter J.C., Han C., Tapia R., Land M., Hauser L.,
RA Kyrpides N., Ivanova N., Mikhailova N., Pagani I., Cadillo-Quiroz H.,
RA Imachi H., Zinder S., Liu W., Woyke T.;
RT "Complete sequence of Methanobacterium sp. AL-21.";
RL Submitted (FEB-2011) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:ADZ08335.1, ECO:0000313|Proteomes:UP000007490}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AL-21 {ECO:0000313|EMBL:ADZ08335.1,
RC ECO:0000313|Proteomes:UP000007490};
RX PubMed=24449792; DOI=10.1099/ijs.0.059964-0;
RA Cadillo-Quiroz H., Brauer S.L., Goodson N., Yavitt J.B., Zinder S.H.;
RT "Methanobacterium paludis sp. nov. and a novel strain of Methanobacterium
RT lacus isolated from northern peatlands.";
RL Int. J. Syst. Evol. Microbiol. 64:1473-1480(2014).
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; CP002551; ADZ08335.1; -; Genomic_DNA.
DR RefSeq; WP_013643686.1; NC_015216.1.
DR AlphaFoldDB; F0T7A6; -.
DR STRING; 877455.Metbo_0082; -.
DR GeneID; 10276505; -.
DR KEGG; mel:Metbo_0082; -.
DR eggNOG; arCOG00106; Archaea.
DR HOGENOM; CLU_022752_2_1_2; -.
DR OrthoDB; 8896at2157; -.
DR UniPathway; UPA00148; UER00231.
DR Proteomes; UP000007490; 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:UP000007490}.
FT DOMAIN 4..189
FT /note="CobQ/CobB/MinD/ParA nucleotide binding"
FT /evidence="ECO:0000259|Pfam:PF01656"
FT DOMAIN 248..433
FT /note="CobB/CobQ-like glutamine amidotransferase"
FT /evidence="ECO:0000259|Pfam:PF07685"
FT ACT_SITE 330
FT /note="Nucleophile"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
FT SITE 429
FT /note="Increases nucleophilicity of active site Cys"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
SQ SEQUENCE 451 AA; 49464 MW; 159B4D63AA7F5F71 CRC64;
MRAVIAGTGS AVGKTTISTG IMSALSSEYN VQPFKAGPDY IDPTYHGLAT GNVSRNLDSF
FMSDGQIREA FERGINSSKS DMGIIEGVRG LYEGISPLGE VGSTASVAKA LNAPVILILN
SRSLVKSAAA VVIGFKTLDP SIRIDGVILN YVKNKKHYLK TKEAVEKLSD TPVIGGIPRK
EAITVEQRHL GLVPAVERQN ILQSIEKWGE EMTNNIDLDA LIAIMKNSGD LPRGREPIWE
EGNKKPVKIG VAMDEVFTFY YKENIESLEA NKAKIIPFSP IHDETIPDVD GLYIGGGYPE
IFAKELSRNS SMRKSILKFH NDAHPIYAEC GGLMYLSNSI NGHSMCNVFK YPSKMTKNVQ
ALSYVISEAQ NDNIILNKGE QFKGHEFHYS KIEVDGNNPK YAFKILRGRG IDGSNDGLME
NNTVASYVHT HVAACPQFGL NFARNSHNKD S
//
