BIOD_MYCVP
ID BIOD_MYCVP Reviewed; 226 AA.
AC A1T8U7;
DT 11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT 06-FEB-2007, sequence version 1.
DT 03-AUG-2022, entry version 92.
DE RecName: Full=ATP-dependent dethiobiotin synthetase BioD {ECO:0000255|HAMAP-Rule:MF_00336};
DE EC=6.3.3.3 {ECO:0000255|HAMAP-Rule:MF_00336};
DE AltName: Full=DTB synthetase {ECO:0000255|HAMAP-Rule:MF_00336};
DE Short=DTBS {ECO:0000255|HAMAP-Rule:MF_00336};
DE AltName: Full=Dethiobiotin synthase {ECO:0000255|HAMAP-Rule:MF_00336};
GN Name=bioD {ECO:0000255|HAMAP-Rule:MF_00336}; OrderedLocusNames=Mvan_2790;
OS Mycolicibacterium vanbaalenii (strain DSM 7251 / JCM 13017 / BCRC 16820 /
OS KCTC 9966 / NRRL B-24157 / PYR-1) (Mycobacterium vanbaalenii).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycolicibacterium.
OX NCBI_TaxID=350058;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 7251 / JCM 13017 / BCRC 16820 / KCTC 9966 / NRRL B-24157 /
RC PYR-1;
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S.,
RA Singan V., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N.,
RA Anderson I.J., Miller C., Richardson P.;
RT "Complete sequence of Mycobacterium vanbaalenii PYR-1.";
RL Submitted (DEC-2006) to the EMBL/GenBank/DDBJ databases.
CC -!- FUNCTION: Catalyzes a mechanistically unusual reaction, the ATP-
CC dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-
CC diaminopelargonic acid (DAPA, also called 7,8-diammoniononanoate) to
CC form a ureido ring. {ECO:0000255|HAMAP-Rule:MF_00336}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(7R,8S)-7,8-diammoniononanoate + ATP + CO2 = (4R,5S)-
CC dethiobiotin + ADP + 3 H(+) + phosphate; Xref=Rhea:RHEA:15805,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:30616,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:149469, ChEBI:CHEBI:149473,
CC ChEBI:CHEBI:456216; EC=6.3.3.3; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_00336};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00336};
CC -!- PATHWAY: Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-
CC diaminononanoate: step 1/2. {ECO:0000255|HAMAP-Rule:MF_00336}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00336}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00336}.
CC -!- SIMILARITY: Belongs to the dethiobiotin synthetase family.
CC {ECO:0000255|HAMAP-Rule:MF_00336}.
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DR EMBL; CP000511; ABM13597.1; -; Genomic_DNA.
DR RefSeq; WP_011780005.1; NC_008726.1.
DR AlphaFoldDB; A1T8U7; -.
DR SMR; A1T8U7; -.
DR STRING; 350058.Mvan_2790; -.
DR EnsemblBacteria; ABM13597; ABM13597; Mvan_2790.
DR KEGG; mva:Mvan_2790; -.
DR eggNOG; COG0132; Bacteria.
DR HOGENOM; CLU_072551_1_0_11; -.
DR OMA; SPHWAAE; -.
DR OrthoDB; 1739932at2; -.
DR UniPathway; UPA00078; UER00161.
DR Proteomes; UP000009159; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0004141; F:dethiobiotin synthase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0000287; F:magnesium ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0009102; P:biotin biosynthetic process; IEA:UniProtKB-UniRule.
DR Gene3D; 3.40.50.300; -; 1.
DR HAMAP; MF_00336; BioD; 1.
DR InterPro; IPR004472; DTB_synth_BioD.
DR InterPro; IPR027417; P-loop_NTPase.
DR InterPro; IPR002347; SDR_fam.
DR PANTHER; PTHR43210; PTHR43210; 1.
DR PIRSF; PIRSF006755; DTB_synth; 1.
DR PRINTS; PR00081; GDHRDH.
DR SUPFAM; SSF52540; SSF52540; 1.
DR TIGRFAMs; TIGR00347; bioD; 1.
PE 3: Inferred from homology;
KW ATP-binding; Biotin biosynthesis; Cytoplasm; Ligase; Magnesium;
KW Metal-binding; Nucleotide-binding; Reference proteome.
FT CHAIN 1..226
FT /note="ATP-dependent dethiobiotin synthetase BioD"
FT /id="PRO_0000302531"
FT ACT_SITE 37
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 12..17
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 16
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 41
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 49
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 49
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 108..111
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 108
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 197..199
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
SQ SEQUENCE 226 AA; 22914 MW; 8E35A09390D3B3B1 CRC64;
MSVLVVTGTG TGIGKTVATA ALACHARLHG IDVAVCKPVQ TGTRDGDDDL AEVARLAGVT
ELHSLARFPE PLAPLAAARR SGAELPTRAQ ILDLITAADR PGRLTLVEGA GGLLVEIASD
GSTLRDVAAD LGAPVLTVVA PGLGTLNHTV LTLEALAHRQ ISSAGLVIGA WPAQPGVAEI
DNRDALSRLA PVRAALPAGA GSLGRADFER LSVDAFDPSW VEGLAA
