ID A0A1G9D765_9RHOB Unreviewed; 432 AA.
AC A0A1G9D765;
DT 22-NOV-2017, integrated into UniProtKB/TrEMBL.
DT 22-NOV-2017, sequence version 1.
DT 27-MAR-2024, entry version 23.
DE RecName: Full=Hydrogenobyrinate a,c-diamide synthase {ECO:0000256|HAMAP-Rule:MF_00027};
DE EC=6.3.5.9 {ECO:0000256|HAMAP-Rule:MF_00027};
DE AltName: Full=Hydrogenobyrinic acid a,c-diamide synthase {ECO:0000256|HAMAP-Rule:MF_00027};
GN Name=cobB {ECO:0000256|HAMAP-Rule:MF_00027};
GN ORFNames=SAMN05216257_103368 {ECO:0000313|EMBL:SDK59545.1};
OS Meinhardsimonia xiamenensis.
OC Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodobacterales;
OC Paracoccaceae; Meinhardsimonia.
OX NCBI_TaxID=990712 {ECO:0000313|EMBL:SDK59545.1, ECO:0000313|Proteomes:UP000199328};
RN [1] {ECO:0000313|Proteomes:UP000199328}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CGMCC 1.10789 {ECO:0000313|Proteomes:UP000199328};
RA Varghese N., Submissions S.;
RL Submitted (OCT-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 hydrogenobyrinate, using either L-
CC glutamine or ammonia as the nitrogen source. {ECO:0000256|HAMAP-
CC Rule:MF_00027}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2 ATP + 2 H2O + hydrogenobyrinate + 2 L-glutamine = 2 ADP + 2
CC H(+) + hydrogenobyrinate a,c-diamide + 2 L-glutamate + 2 phosphate;
CC Xref=Rhea:RHEA:12544, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:29985, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474,
CC ChEBI:CHEBI:58359, ChEBI:CHEBI:77873, ChEBI:CHEBI:77874,
CC ChEBI:CHEBI:456216; EC=6.3.5.9; 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 precorrin-2 (aerobic route): step 9/10.
CC {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 hydrogenobyrinate and catalyzes the
CC ultimate 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 hydrogenobyrinate are
CC activated for nucleophilic attack via formation of a phosphorylated
CC intermediate by ATP. CobB catalyzes first the amidation of the c-
CC carboxylate, and then that of the a-carboxylate. {ECO:0000256|HAMAP-
CC Rule:MF_00027}.
CC -!- SIMILARITY: Belongs to the CobB/CbiA family. {ECO:0000256|HAMAP-
CC Rule:MF_00027}.
CC -!- SIMILARITY: Belongs to the CobB/CobQ family. CobQ subfamily.
CC {ECO:0000256|ARBA:ARBA00006205}.
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DR EMBL; FNFV01000003; SDK59545.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A1G9D765; -.
DR STRING; 990712.SAMN05216257_103368; -.
DR OrthoDB; 9764035at2; -.
DR UniPathway; UPA00148; UER00220.
DR Proteomes; UP000199328; 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:InterPro.
DR GO; GO:0043802; F:hydrogenobyrinic acid a,c-diamide synthase (glutamine-hydrolysing) 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 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:UP000199328}.
FT DOMAIN 6..185
FT /note="CobQ/CobB/MinD/ParA nucleotide binding"
FT /evidence="ECO:0000259|Pfam:PF01656"
FT DOMAIN 239..420
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 418
FT /note="Increases nucleophilicity of active site Cys"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
SQ SEQUENCE 432 AA; 44750 MW; 9AB3CF17559BDAA2 CRC64;
MTGRGLIIAA PASGSGKTTL TLGLLRALAR RGTPVRGAKS GPDYIDPRFH AAACGVECLN
LDAWAMSAEE IRARAAGPGL LLIEGAMGLF DGAPPDGRGA TADLARILGL PVVLIVDAAR
MAQSVAPLVA GFARFDAQVE IAGVILNRVG SPRHAQMLRR ALAPSGLPVL GALPREPRLA
HPSRHLGLVQ AGERADLEAF LDSAAEAVAA AVDLEALAAL ARPLPEPGGW RAPLPPAQRI
AVARDAAFGF AYPHWLADWR AGGAEIVFFS PLADEPVPQA DLVFLPGGYP ELHAGRIAAA
RRFLASLRGA AQTAQIYGEC GGYMVLGEAL IDAEGTPHAM AGLLPLLTSF AERRLTLGYR
RLAALAGPFP GHHLGHEFHY ATTMKAEGAP LFAAEDAEGN ALPPMGLVAG RVAGSFAHII
PTPGPADRAG QS
//
