BIOD_BURCC
ID BIOD_BURCC Reviewed; 239 AA.
AC B1JZE0;
DT 14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT 29-APR-2008, sequence version 1.
DT 03-AUG-2022, entry version 80.
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};
GN OrderedLocusNames=Bcenmc03_2948;
OS Burkholderia cenocepacia (strain MC0-3).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Burkholderiaceae; Burkholderia; Burkholderia cepacia complex.
OX NCBI_TaxID=406425;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=MC0-3;
RA Copeland A., Lucas S., Lapidus A., Barry K., Bruce D., Goodwin L.,
RA Glavina del Rio T., Dalin E., Tice H., Pitluck S., Chain P., Malfatti S.,
RA Shin M., Vergez L., Schmutz J., Larimer F., Land M., Hauser L.,
RA Kyrpides N., Mikhailova N., Tiedje J., Richardson P.;
RT "Complete sequence of chromosome 1 of Burkholderia cenocepacia MC0-3.";
RL Submitted (FEB-2008) 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; CP000958; ACA92106.1; -; Genomic_DNA.
DR RefSeq; WP_012329325.1; NC_010508.1.
DR AlphaFoldDB; B1JZE0; -.
DR SMR; B1JZE0; -.
DR EnsemblBacteria; ACA92106; ACA92106; Bcenmc03_2948.
DR KEGG; bcm:Bcenmc03_2948; -.
DR HOGENOM; CLU_072551_0_0_4; -.
DR OMA; SPHWAAE; -.
DR UniPathway; UPA00078; UER00161.
DR Proteomes; UP000002169; Chromosome 1.
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 PANTHER; PTHR43210; PTHR43210; 1.
DR PIRSF; PIRSF006755; DTB_synth; 1.
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.
FT CHAIN 1..239
FT /note="ATP-dependent dethiobiotin synthetase BioD"
FT /id="PRO_1000119861"
FT ACT_SITE 40
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 15..20
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 19
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 57
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 57
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 118..121
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 118
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT BINDING 178..179
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
SQ SEQUENCE 239 AA; 25189 MW; DB74C40F53EFAE98 CRC64;
MSAPLSVFVT GTDTEIGKTF VSAAMLHGFA RHGLRAAALK PIAAGAYERD GVWRNEDADQ
LDAAANVALP PELRTPFLLK APAAPHIVAA QEGVTLDLDT IVACHREALT RADVVVVEGV
GGFRVPLNDT QDTADLAVAL GLPVVLVVGV RLGCISHALL TADAIRQRGL TLAGWVANHV
DPAMSFADEN VATIRDWLAR ERRAPLIGRI AHMTPAAPES AAAMLDIAAL VESLRTARH
