CBIA_METAC
ID CBIA_METAC Reviewed; 497 AA.
AC Q8TK00;
DT 22-NOV-2017, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2002, sequence version 1.
DT 03-AUG-2022, entry version 112.
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:27846569};
DE EC=6.3.5.12 {ECO:0000255|HAMAP-Rule:MF_00027, ECO:0000269|PubMed:27846569};
DE AltName: Full=Ni-sirohydrochlorin a,c-diamide synthetase {ECO:0000255|HAMAP-Rule:MF_00027, ECO:0000303|PubMed:27846569};
GN Name=cbiA {ECO:0000255|HAMAP-Rule:MF_00027};
GN Synonyms=cfbB {ECO:0000255|HAMAP-Rule:MF_00027,
GN ECO:0000303|PubMed:27846569};
GN OrderedLocusNames=MA_3626 {ECO:0000312|EMBL:AAM06981.1};
OS Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 /
OS C2A).
OC Archaea; Euryarchaeota; Stenosarchaea group; Methanomicrobia;
OC Methanosarcinales; Methanosarcinaceae; Methanosarcina.
OX NCBI_TaxID=188937;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 35395 / DSM 2834 / JCM 12185 / C2A
RC {ECO:0000312|Proteomes:UP000002487};
RX PubMed=11932238; DOI=10.1101/gr.223902;
RA Galagan J.E., Nusbaum C., Roy A., Endrizzi M.G., Macdonald P., FitzHugh W.,
RA Calvo S., Engels R., Smirnov S., Atnoor D., Brown A., Allen N., Naylor J.,
RA Stange-Thomann N., DeArellano K., Johnson R., Linton L., McEwan P.,
RA McKernan K., Talamas J., Tirrell A., Ye W., Zimmer A., Barber R.D.,
RA Cann I., Graham D.E., Grahame D.A., Guss A.M., Hedderich R.,
RA Ingram-Smith C., Kuettner H.C., Krzycki J.A., Leigh J.A., Li W., Liu J.,
RA Mukhopadhyay B., Reeve J.N., Smith K., Springer T.A., Umayam L.A.,
RA White O., White R.H., de Macario E.C., Ferry J.G., Jarrell K.F., Jing H.,
RA Macario A.J.L., Paulsen I.T., Pritchett M., Sowers K.R., Swanson R.V.,
RA Zinder S.H., Lander E., Metcalf W.W., Birren B.;
RT "The genome of Methanosarcina acetivorans reveals extensive metabolic and
RT physiological diversity.";
RL Genome Res. 12:532-542(2002).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, AND COFACTOR.
RC STRAIN=ATCC 35395 / DSM 2834 / JCM 12185 / C2A;
RX PubMed=27846569; DOI=10.1126/science.aag2947;
RA Zheng K., Ngo P.D., Owens V.L., Yang X.P., Mansoorabadi S.O.;
RT "The biosynthetic pathway of coenzyme F430 in methanogenic and
RT methanotrophic archaea.";
RL Science 354:339-342(2016).
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:27846569). 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:27846569).
CC {ECO:0000255|HAMAP-Rule:MF_00027, ECO:0000269|PubMed:27846569}.
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:27846569};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00027,
CC ECO:0000305|PubMed:27846569};
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, ECO:0000305}.
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DR EMBL; AE010299; AAM06981.1; -; Genomic_DNA.
DR RefSeq; WP_011023534.1; NC_003552.1.
DR AlphaFoldDB; Q8TK00; -.
DR STRING; 188937.MA_3626; -.
DR EnsemblBacteria; AAM06981; AAM06981; MA_3626.
DR GeneID; 1475519; -.
DR KEGG; mac:MA_3626; -.
DR HOGENOM; CLU_022752_2_1_2; -.
DR InParanoid; Q8TK00; -.
DR OMA; MYLTNSI; -.
DR OrthoDB; 14023at2157; -.
DR PhylomeDB; Q8TK00; -.
DR BioCyc; MetaCyc:MON-20114; -.
DR UniPathway; UPA00148; UER00231.
DR Proteomes; UP000002487; 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 1: Evidence at protein level;
KW ATP-binding; Cobalamin biosynthesis; Glutamine amidotransferase; Ligase;
KW Magnesium; Methanogenesis; Nucleotide-binding; Reference proteome.
FT CHAIN 1..497
FT /note="Cobyrinate a,c-diamide synthase"
FT /id="PRO_0000442458"
FT DOMAIN 273..478
FT /note="GATase cobBQ-type"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00027"
FT ACT_SITE 355
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00027"
FT SITE 470
FT /note="Increases nucleophilicity of active site Cys"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00027"
SQ SEQUENCE 497 AA; 53485 MW; 546AB64C28633010 CRC64;
MSHSKQSGTE AGSIPRVLIS ADRSSSGKTT ISMGLMAALV SRGYKVQPFK VALDYIDPSY
HTEITGRFCR NLDGYLMDEN GILDVYSHAC ETGSGADIAI IEGVRGLYEG FEGLSDLGST
AQIAKILKCP VVFVINARSI TRSAAALISG YKNFDPDVEI AGVILNNIGG RRHAQKAKEA
IEHYTGVPVI GIIPRDPSMQ ISMRHLGLMP ALEGRRRLGD GGFEDRLRGI EEIINKGIDV
DRFLEIAGSA KSLTSPENSI FSPAAGAGSP RPRIGIALDE AFNFYYRDNI DLLELAGAEI
VYFSPVNDPE LPDVDGLYIG GGYPELFAAE LEANESMRRS IKEASAAGMP IYAECGGLMY
LTEKISTGVP GKGTYHDASM PESTYIMVGA LPGHTIMGQT RVVSYNIGTL DRDCLIGKEG
NSFKGHEFHH SEIREIPEYA EFAIALLRGT GIKGDRDGLI VGNTLGSYAH LHGVAYRELA
GSLVEAAGKF RASRAPR
