ID E6J7J5_9ACTN Unreviewed; 512 AA.
AC E6J7J5;
DT 08-MAR-2011, integrated into UniProtKB/TrEMBL.
DT 08-MAR-2011, sequence version 1.
DT 27-MAR-2024, entry version 58.
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=ES5_05962 {ECO:0000313|EMBL:EFV92432.1};
OS Dietzia cinnamea P4.
OC Bacteria; Actinomycetota; Actinomycetes; Mycobacteriales; Dietziaceae;
OC Dietzia.
OX NCBI_TaxID=910954 {ECO:0000313|EMBL:EFV92432.1, ECO:0000313|Proteomes:UP000004165};
RN [1] {ECO:0000313|EMBL:EFV92432.1, ECO:0000313|Proteomes:UP000004165}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=P4 {ECO:0000313|EMBL:EFV92432.1,
RC ECO:0000313|Proteomes:UP000004165};
RX PubMed=21901521; DOI=10.1007/s10482-011-9633-7;
RA Procopio L., Alvarez V.M., Jurelevicius D.A., Hansen L., Sorensen S.J.,
RA Cardoso J.S., Padula M., Leitao A.C., Seldin L., van Elsas J.D.;
RT "Insight from the draft genome of Dietzia cinnamea P4 reveals mechanisms of
RT survival in complex tropical soil habitats and biotechnology potential.";
RL Antonie Van Leeuwenhoek 101:289-302(2012).
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 -!- 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:EFV92432.1}.
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DR EMBL; AEKG01000116; EFV92432.1; -; Genomic_DNA.
DR RefSeq; WP_007628513.1; NZ_AEKG01000116.1.
DR AlphaFoldDB; E6J7J5; -.
DR UniPathway; UPA00148; UER00220.
DR Proteomes; UP000004165; 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 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}.
FT DOMAIN 8..207
FT /note="CobQ/CobB/MinD/ParA nucleotide binding"
FT /evidence="ECO:0000259|Pfam:PF01656"
FT DOMAIN 277..477
FT /note="CobB/CobQ-like glutamine amidotransferase"
FT /evidence="ECO:0000259|Pfam:PF07685"
FT REGION 422..453
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 359
FT /note="Nucleophile"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
FT SITE 471
FT /note="Increases nucleophilicity of active site Cys"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
SQ SEQUENCE 512 AA; 51854 MW; 188D0A93AD6453F6 CRC64;
MVSELPRLVV AAPASGHGKT TVATGLMAAL RRTGLEVSGH KVGPDYIDPG YHALATGRPG
RNLDPHLVGE ERIVPLLLHG ADAGGGAGGA GIGARRPADV AVIEGVMGLY DGHIGGDGFA
STAHVAALTA TPVVLVVDIS HASRTIAATV LGMATFDPDV RIAGVVLNKA GSVRHSDEVR
RALAPLGIPV LGVLQRDDDV TAPSRHLGLV PAAERPEAAR SLDHLAGKVA ASIDLEAVMR
IARSAPPLRG QVWSAQEAVA GGGRGSGGDD DKGRPLIAVA GGRAFTFRYA ETVELLKAAG
CSVAPFDPLA DEALPDGTAG IYLGGGFPEV HAGDLAANEP MLWALRAATS AGVPTVAECA
GLLYLCRSLD GVPMVGAIDA DAAMAPRLTL AYRRSTAVAD SVLAAAGTEV TGHEFHRTAV
TPAAGADTEP RPTGQGSGAG PGPGLSASPA WTSSAGPEGF VTGSIHASYL HTHWAGHPAL
AVRFAELVRA FAGAPQPPRR ASGRRPAQLA RP
//
