ID A0A161WVB2_9CLOT Unreviewed; 443 AA.
AC A0A161WVB2;
DT 06-JUL-2016, integrated into UniProtKB/TrEMBL.
DT 06-JUL-2016, sequence version 1.
DT 27-MAR-2024, entry version 33.
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=cobB_1 {ECO:0000313|EMBL:KZL90828.1};
GN Synonyms=cbiA {ECO:0000256|HAMAP-Rule:MF_00027};
GN ORFNames=CLMAG_37390 {ECO:0000313|EMBL:KZL90828.1};
OS Clostridium magnum DSM 2767.
OC Bacteria; Bacillota; Clostridia; Eubacteriales; Clostridiaceae;
OC Clostridium.
OX NCBI_TaxID=1121326 {ECO:0000313|EMBL:KZL90828.1, ECO:0000313|Proteomes:UP000076603};
RN [1] {ECO:0000313|EMBL:KZL90828.1, ECO:0000313|Proteomes:UP000076603}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 2767 {ECO:0000313|EMBL:KZL90828.1,
RC ECO:0000313|Proteomes:UP000076603};
RA Poehlein A., Uhlig R., Fischer R., Bahl H., Daniel R.;
RT "Genome sequence of Clostridium magnum DSM 2767.";
RL Submitted (APR-2016) to the EMBL/GenBank/DDBJ databases.
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|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 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}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:KZL90828.1}.
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DR EMBL; LWAE01000004; KZL90828.1; -; Genomic_DNA.
DR RefSeq; WP_066625665.1; NZ_LWAE01000004.1.
DR AlphaFoldDB; A0A161WVB2; -.
DR STRING; 1121326.CLMAG_37390; -.
DR PATRIC; fig|1121326.3.peg.3783; -.
DR OrthoDB; 9764035at2; -.
DR UniPathway; UPA00148; UER00231.
DR Proteomes; UP000076603; Unassembled WGS sequence.
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; 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 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 Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|HAMAP-
KW Rule:MF_00027}; Reference proteome {ECO:0000313|Proteomes:UP000076603}.
FT DOMAIN 5..183
FT /note="CobQ/CobB/MinD/ParA nucleotide binding"
FT /evidence="ECO:0000259|Pfam:PF01656"
FT DOMAIN 238..430
FT /note="CobB/CobQ-like glutamine amidotransferase"
FT /evidence="ECO:0000259|Pfam:PF07685"
FT ACT_SITE 320
FT /note="Nucleophile"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
FT SITE 425
FT /note="Increases nucleophilicity of active site Cys"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
SQ SEQUENCE 443 AA; 49578 MW; 1A9F4924ED0B07C9 CRC64;
MKGLVISSNS SGGGKTTVTL GIMKALMKKG FDVQGYKVGP DYIDPAFHSY ITGKASRNLD
LFLMGEEGVK ASFSRGIGDL GIVEGVMGLY DGKGIDSEYS TAHVARVLNL PILLVITPKA
QSATLCAELN GLLNFEKVNI SGVIFNNISE KYYKLLKAAV EKNCNIKVFG YVPKNEKLSL
KSRHLGLVQS SEVDDLKEKI DLCSDLILEH VDVETLLGYF KKTENYDDKY HLESRAIRIA
VAYDKAFSFY YKENLELLEE AGEVVYFSPL KDKKLPDNID FLYIGGGYPE VFIEELSKNK
SMLNSIKESL EKGLKCYSEC GGLMYLTEAI ESIDGEKNFS TVGFFKGTTH MTKTLQNFGY
ARIKVEKKNN VLSTGMEINC HEFHKSYVSL EDEKVYLLTK EMYDGELKKW NCGYVKNNVL
GAYGHVHFFG NIDILKNLLN LDV
//
