ID M1PHU8_DESSD Unreviewed; 458 AA.
AC M1PHU8;
DT 01-MAY-2013, integrated into UniProtKB/TrEMBL.
DT 01-MAY-2013, sequence version 1.
DT 24-JAN-2024, entry version 56.
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};
GN Name=cbiA {ECO:0000256|HAMAP-Rule:MF_00027};
GN OrderedLocusNames=UWK_02639 {ECO:0000313|EMBL:AGF79175.1};
OS Desulfocapsa sulfexigens (strain DSM 10523 / SB164P1).
OC Bacteria; Thermodesulfobacteriota; Desulfobulbia; Desulfobulbales;
OC Desulfocapsaceae; Desulfocapsa.
OX NCBI_TaxID=1167006 {ECO:0000313|EMBL:AGF79175.1, ECO:0000313|Proteomes:UP000011721};
RN [1] {ECO:0000313|Proteomes:UP000011721}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 10523 / SB164P1 {ECO:0000313|Proteomes:UP000011721};
RX PubMed=23961312; DOI=10.4056/sigs.3777412;
RA Finster K.W., Kjeldsen K.U., Kube M., Reinhardt R., Mussmann M., Amann R.,
RA Schreiber L.;
RT "Complete genome sequence of Desulfocapsa sulfexigens, a marine
RT deltaproteobacterium specialized in disproportionating inorganic sulfur
RT compounds.";
RL Stand. Genomic Sci. 8:58-68(2013).
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. {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|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 and catalyzes the ultimate
CC synthesis of the diamide product. The ammonia produced via the
CC glutaminase domain is probably translocated to the adjacent domain via
CC a molecular tunnel, where it reacts with an activated intermediate.
CC {ECO:0000256|HAMAP-Rule:MF_00027}.
CC -!- MISCELLANEOUS: The a and c carboxylates of cobyrinate are activated for
CC nucleophilic attack via formation of a phosphorylated intermediate by
CC ATP. CbiA catalyzes first the amidation of the c-carboxylate, and then
CC that of the a-carboxylate. {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; CP003985; AGF79175.1; -; Genomic_DNA.
DR RefSeq; WP_015404861.1; NC_020304.1.
DR AlphaFoldDB; M1PHU8; -.
DR STRING; 1167006.UWK_02639; -.
DR KEGG; dsf:UWK_02639; -.
DR PATRIC; fig|1167006.5.peg.2858; -.
DR eggNOG; COG1797; Bacteria.
DR HOGENOM; CLU_022752_2_1_7; -.
DR OMA; MYLTNSI; -.
DR OrthoDB; 9764035at2; -.
DR UniPathway; UPA00148; UER00231.
DR Proteomes; UP000011721; 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 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_synth.
DR InterPro; IPR029062; Class_I_gatase-like.
DR InterPro; IPR011698; GATase_3.
DR InterPro; IPR027417; P-loop_NTPase.
DR NCBIfam; TIGR00379; cobB; 1.
DR PANTHER; PTHR43873; COBYRINATE A,C-DIAMIDE SYNTHASE; 1.
DR PANTHER; PTHR43873:SF1; COBYRINATE A,C-DIAMIDE SYNTHASE; 1.
DR Pfam; PF13500; AAA_26; 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|HAMAP-Rule:MF_00027};
KW 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|HAMAP-Rule:MF_00027, ECO:0000313|EMBL:AGF79175.1};
KW Magnesium {ECO:0000256|HAMAP-Rule:MF_00027};
KW Nucleotide-binding {ECO:0000256|HAMAP-Rule:MF_00027};
KW Reference proteome {ECO:0000313|Proteomes:UP000011721}.
FT DOMAIN 245..436
FT /note="CobB/CobQ-like glutamine amidotransferase"
FT /evidence="ECO:0000259|Pfam:PF07685"
FT ACT_SITE 327
FT /note="Nucleophile"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
FT SITE 431
FT /note="Increases nucleophilicity of active site Cys"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
SQ SEQUENCE 458 AA; 49881 MW; 29F4C3C45321F174 CRC64;
MTKGIVVAGL AGGSGKSVVS VGLTAALARQ GKFVVPFKKG PDYIDAGWMK LAAGRNCYNL
DPYLMSEESI KASLLCHSEG ADLVVLEGNR GLFDGVNVDG GYSTAELALS LNLPILLVVN
CTKTTRTVAA MVLGCMKLDE RVDIRGVVLN QIGTKRHQSI VTQAVEKYTG LPVLGAIPRM
KYDIFPMRHL GVTPHQEYEG SEEAMQLLAE TAAEHLDLER IQEVMEPIGC RKTVVPAHPP
ENKLRIGLLM DAAFQFYYSE NLEALEQEGA ELIAIDAMVE DVLPELDGLY IGGGFPETSA
GALAANTSFR DSIKTAAETG LPIYAECGGL IYLGESIELE GEVYPLAGVF PVRFGMSQKP
QAHGYSIFTV EGENPFYEKG SEIKGHEFRY STIIDWPGDS DDLPLKMTRG VGFSKGREGL
VMNNVLALYT HIHALGTPEW ARGFMRRCRE VKEEGLRE
//