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CBIA_METST
ID   CBIA_METST              Reviewed;         453 AA.
AC   Q2NHQ3;
DT   15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT   07-FEB-2006, sequence version 1.
DT   25-MAY-2022, entry version 88.
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=Msp_0162;
OS   Methanosphaera stadtmanae (strain ATCC 43021 / DSM 3091 / JCM 11832 /
OS   MCB-3).
OC   Archaea; Euryarchaeota; Methanomada group; Methanobacteria;
OC   Methanobacteriales; Methanobacteriaceae; Methanosphaera.
OX   NCBI_TaxID=339860;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 43021 / DSM 3091 / JCM 11832 / MCB-3;
RX   PubMed=16385054; DOI=10.1128/jb.188.2.642-658.2006;
RA   Fricke W.F., Seedorf H., Henne A., Kruer M., Liesegang H., Hedderich R.,
RA   Gottschalk G., Thauer R.K.;
RT   "The genome sequence of Methanosphaera stadtmanae reveals why this human
RT   intestinal archaeon is restricted to methanol and H2 for methane formation
RT   and ATP synthesis.";
RL   J. Bacteriol. 188:642-658(2006).
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; CP000102; ABC56580.1; -; Genomic_DNA.
DR   RefSeq; WP_011405779.1; NC_007681.1.
DR   AlphaFoldDB; Q2NHQ3; -.
DR   SMR; Q2NHQ3; -.
DR   STRING; 339860.Msp_0162; -.
DR   EnsemblBacteria; ABC56580; ABC56580; Msp_0162.
DR   GeneID; 41324735; -.
DR   KEGG; mst:Msp_0162; -.
DR   eggNOG; arCOG00106; Archaea.
DR   HOGENOM; CLU_022752_2_1_2; -.
DR   OMA; MYLTNSI; -.
DR   OrthoDB; 14023at2157; -.
DR   UniPathway; UPA00148; UER00231.
DR   Proteomes; UP000001931; 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; Reference proteome.
FT   CHAIN           1..453
FT                   /note="Cobyrinate a,c-diamide synthase"
FT                   /id="PRO_1000002293"
FT   DOMAIN          250..440
FT                   /note="GATase cobBQ-type"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00027"
FT   ACT_SITE        332
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00027"
FT   SITE            432
FT                   /note="Increases nucleophilicity of active site Cys"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00027"
SQ   SEQUENCE   453 AA;  50720 MW;  09423AFEAA664D2C CRC64;
     MKRVVLTGTG SGVGKTTIAT GIMKALSDEH KIQPFKVGPD YIDPSYHNCA TGVSSRNLDS
     FFMSDGQIRQ SFKNGMTSSH ADYGIIEGVR GLYEGISPTN DIGSTSSIAK ALNSPVILII
     NSRSLVRSAA AMTLGFKALD SRIDIEGVIL NNVKSQKHYL KTKEAVEKLA NTRVLGGIER
     DNSISMEQRH LGLIPAVEQE RISGLVEKWG ELIRENIDLD ALMEIMDNSN PIINEYEPIW
     SPNKTKHKTR IAVPFDEAFN FYYKENLEAL EYNNAKIEYF SPIHDEQLPS VDALYIGGGY
     PEIFKKELSK NTTMLESIKE FSQDNHPIYA ECGGLMYLCK TIDSLPMVDV FPYHSMLTKR
     VQGLSYTIAH VQRDNPILKK NTTYHGHEFH YSKVEYTGSN SNDFAFSMRR GVGITGKYDG
     LLKNNTLASY IHTHTACLPD FGYNFTQSAY ENK
 
 
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