CBIA_METBF
ID CBIA_METBF Reviewed; 494 AA.
AC Q46FL0;
DT 22-NOV-2017, integrated into UniProtKB/Swiss-Prot.
DT 13-SEP-2005, sequence version 1.
DT 25-MAY-2022, entry version 111.
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, ECO:0000303|PubMed:28225763};
DE EC=6.3.5.12 {ECO:0000255|HAMAP-Rule:MF_00027, ECO:0000269|PubMed:28225763};
DE AltName: Full=Ni-sirohydrochlorin a,c-diamide synthetase {ECO:0000255|HAMAP-Rule:MF_00027, ECO:0000303|PubMed:28225763};
GN Name=cbiA {ECO:0000255|HAMAP-Rule:MF_00027};
GN Synonyms=cfbB {ECO:0000255|HAMAP-Rule:MF_00027,
GN ECO:0000303|PubMed:28225763};
GN OrderedLocusNames=Mbar_A0348 {ECO:0000312|EMBL:AAZ69332.1};
OS Methanosarcina barkeri (strain Fusaro / DSM 804).
OC Archaea; Euryarchaeota; Stenosarchaea group; Methanomicrobia;
OC Methanosarcinales; Methanosarcinaceae; Methanosarcina.
OX NCBI_TaxID=269797;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Fusaro / DSM 804;
RX PubMed=16980466; DOI=10.1128/jb.00810-06;
RA Maeder D.L., Anderson I., Brettin T.S., Bruce D.C., Gilna P., Han C.S.,
RA Lapidus A., Metcalf W.W., Saunders E., Tapia R., Sowers K.R.;
RT "The Methanosarcina barkeri genome: comparative analysis with
RT Methanosarcina acetivorans and Methanosarcina mazei reveals extensive
RT rearrangement within methanosarcinal genomes.";
RL J. Bacteriol. 188:7922-7931(2006).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, COFACTOR, AND
RP SUBSTRATE SPECIFICITY.
RC STRAIN=Fusaro / DSM 804;
RX PubMed=28225763; DOI=10.1038/nature21427;
RA Moore S.J., Sowa S.T., Schuchardt C., Deery E., Lawrence A.D., Ramos J.V.,
RA Billig S., Birkemeyer C., Chivers P.T., Howard M.J., Rigby S.E., Layer G.,
RA Warren M.J.;
RT "Elucidation of the biosynthesis of the methane catalyst coenzyme F430.";
RL Nature 543:78-82(2017).
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 (Potential). Involved in the
CC biosynthesis of the unique nickel-containing tetrapyrrole coenzyme
CC F430, the prosthetic group of methyl-coenzyme M reductase (MCR), which
CC plays a key role in methanogenesis and anaerobic methane oxidation
CC (PubMed:28225763). Catalyzes the ATP-dependent amidation of the two
CC carboxylate groups at positions a and c of Ni-sirohydrochlorin, using
CC L-glutamine or ammonia as the nitrogen source (PubMed:28225763). Also
CC able to use sirohydrochlorin as substrate, but only produces a
CC monoamide species in a much slower reaction (PubMed:28225763). Unable
CC to use other metallosirohydrochlorins such as sirohaem and Co-
CC sirohydrochlorin (PubMed:28225763). {ECO:0000255|HAMAP-Rule:MF_00027,
CC ECO:0000269|PubMed:28225763}.
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 ECO:0000269|PubMed:28225763};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00027,
CC ECO:0000305|PubMed:28225763};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=46 uM for L-glutamine {ECO:0000269|PubMed:28225763};
CC KM=28 uM for ATP {ECO:0000269|PubMed:28225763};
CC Note=kcat is 1.03 min(-1) for ATP as substrate. kcat is 0.78 min(-1)
CC for L-glutamine as substrate. {ECO:0000269|PubMed:28225763};
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; CP000099; AAZ69332.1; -; Genomic_DNA.
DR RefSeq; WP_011305385.1; NC_007355.1.
DR AlphaFoldDB; Q46FL0; -.
DR STRING; 269797.Mbar_A0348; -.
DR EnsemblBacteria; AAZ69332; AAZ69332; Mbar_A0348.
DR GeneID; 3626592; -.
DR KEGG; mba:Mbar_A0348; -.
DR eggNOG; arCOG00106; Archaea.
DR HOGENOM; CLU_022752_2_0_2; -.
DR OMA; MYLTNSI; -.
DR OrthoDB; 14023at2157; -.
DR UniPathway; UPA00148; UER00231.
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; IPR011698; GATase_3.
DR InterPro; IPR027417; P-loop_NTPase.
DR PANTHER; PTHR43873; PTHR43873; 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 1: Evidence at protein level;
KW ATP-binding; Cobalamin biosynthesis; Glutamine amidotransferase; Ligase;
KW Magnesium; Methanogenesis; Nucleotide-binding.
FT CHAIN 1..494
FT /note="Cobyrinate a,c-diamide synthase"
FT /id="PRO_0000442459"
FT DOMAIN 270..475
FT /note="GATase cobBQ-type"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00027"
FT ACT_SITE 352
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00027"
FT SITE 467
FT /note="Increases nucleophilicity of active site Cys"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00027"
SQ SEQUENCE 494 AA; 53786 MW; 88D530FF1A2500C4 CRC64;
MLNDKQSVEN IPRILISADR SSSGKTTISM GLMAALVSRG YKVQPFKVAL DYIDPSYHTE
ITGRFCRNLD GYLMDENGIL DVYTHACEAG EKADIAIIEG VRGLYEGFES LSDLGSTAQI
AKILNCPVIF VINARSITRS SAALINGYRN FDPDVEIAGV ILNNIGSRRH AKKAKEAIEY
YTGVPVIGIV PRDPAMQISM RHLGLMPALE GRRRLGDGGF EARLRGIEEI INKGIDVDRF
MEIAKSAKAL KSPENSVFSS VSDPGAPRPK IGVALDEAFN FYYRDNIDLL NLAGAEIVYF
SPVKDASLPE VDGLYIGGGY PELFAAELEA NESMRQDIKK ASAAGMPIYA ECGGLMYLTE
KISTGVPGKG TYHDASMPES TYSMVGALPG HTIMGQTRVV SYNIGTLNKD CLLGKKYNSF
KGHEFHHSEI REIPEDAEFA ITLSRGTGIK NGMDGLISGN TLGSYAHLHG VAYREFASSL
VEAARNFRDS RVLP
