ID D6Y9M9_THEBD Unreviewed; 510 AA.
AC D6Y9M9;
DT 10-AUG-2010, integrated into UniProtKB/TrEMBL.
DT 10-AUG-2010, sequence version 1.
DT 27-MAR-2024, entry version 75.
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 OrderedLocusNames=Tbis_3370 {ECO:0000313|EMBL:ADG90060.1};
OS Thermobispora bispora (strain ATCC 19993 / DSM 43833 / CBS 139.67 / JCM
OS 10125 / KCTC 9307 / NBRC 14880 / R51).
OC Bacteria; Actinomycetota; Actinomycetes; Streptosporangiales;
OC Streptosporangiaceae; Thermobispora.
OX NCBI_TaxID=469371 {ECO:0000313|EMBL:ADG90060.1, ECO:0000313|Proteomes:UP000006640};
RN [1] {ECO:0000313|EMBL:ADG90060.1, ECO:0000313|Proteomes:UP000006640}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 19993 / DSM 43833 / CBS 139.67 / JCM 10125 / KCTC 9307 /
RC NBRC 14880 / R51 {ECO:0000313|Proteomes:UP000006640};
RG US DOE Joint Genome Institute (JGI-PGF);
RA Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H.,
RA Bruce D., Goodwin L., Pitluck S., Kyrpides N., Mavromatis K., Ivanova N.,
RA Mikhailova N., Chertkov O., Brettin T., Detter J.C., Han C., Larimer F.,
RA Land M., Hauser L., Markowitz V., Cheng J.-F., Hugenholtz P., Woyke T.,
RA Wu D., Jando M., Schneider S., Klenk H.-P., Eisen J.A.;
RT "The complete genome of Thermobispora bispora DSM 43833.";
RL Submitted (JAN-2010) 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}.
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DR EMBL; CP001874; ADG90060.1; -; Genomic_DNA.
DR AlphaFoldDB; D6Y9M9; -.
DR STRING; 469371.Tbis_3370; -.
DR KEGG; tbi:Tbis_3370; -.
DR eggNOG; COG1797; Bacteria.
DR HOGENOM; CLU_022752_1_1_11; -.
DR OrthoDB; 9764035at2; -.
DR UniPathway; UPA00148; UER00220.
DR Proteomes; UP000006640; Chromosome.
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; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 2.
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:UP000006640}.
FT DOMAIN 74..256
FT /note="CobQ/CobB/MinD/ParA nucleotide binding"
FT /evidence="ECO:0000259|Pfam:PF01656"
FT DOMAIN 320..494
FT /note="CobB/CobQ-like glutamine amidotransferase"
FT /evidence="ECO:0000259|Pfam:PF07685"
FT REGION 1..50
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 8..24
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT ACT_SITE 399
FT /note="Nucleophile"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
FT SITE 489
FT /note="Increases nucleophilicity of active site Cys"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_00027"
SQ SEQUENCE 510 AA; 53407 MW; ADDE7F685D4A3862 CRC64;
MGDVSEQHPG RTARHPERRP AAGARRRPPA TGQGHRPGDR LAAQAEDRWP GDRLGAQAED
RATAARSRSS VPRLVIAAPA SDSGKTTVAT GLMAALRARG LRVSPHKVGP DYIDPGYHAL
ATGRPGRNLD PWLTGEESIV PLFLHGARNA DVAVVEGVMG MYDGAGTDDF GSTAHIARLL
GAPVVLVVDA ERQARSVAAL VRGFASFDER VRVAGVILNK VGSPGHGELC RTVLDEIGIP
TLGVIQRVDG VVTPSRHLGL IPAAERRAEA VAAVDRMAEL IARSCDLGAL LAVARSAPPL
TAAPWTPEAG VPDPRPGPVV AVAGGPAFTF GYPEQAELLS AAGAQVVTFD PLRDERLPEG
TGAVVIGGGF PEVYAAELSA NEPLRAELAA FRGPIVAECA GLLYLGRELD GHPMCGRLGI
TARMTDRLAI GYRDAVASAS VVTREGERYR GHEFHRTITE PRHAAPPLFR WPGGADGFGG
PLIAASYLHL HWAAYPELAS RLVAAAAGPG
//
