ID   BIOD_NITWN              Reviewed;         213 AA.
AC   Q3SPW7;
DT   11-SEP-2007, integrated into UniProtKB/Swiss-Prot.
DT   11-OCT-2005, sequence version 1.
DT   09-APR-2025, entry version 114.
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=Nwi_2420;
OS   Nitrobacter winogradskyi (strain ATCC 25391 / DSM 10237 / CIP 104748 /
OS   NCIMB 11846 / Nb-255).
OC   Bacteria; Pseudomonadati; Pseudomonadota; Alphaproteobacteria;
OC   Hyphomicrobiales; Nitrobacteraceae; Nitrobacter.
OX   NCBI_TaxID=323098;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 25391 / DSM 10237 / CIP 104748 / NCIMB 11846 / Nb-255;
RX   PubMed=16517654; DOI=10.1128/aem.72.3.2050-2063.2006;
RA   Starkenburg S.R., Chain P.S.G., Sayavedra-Soto L.A., Hauser L., Land M.L.,
RA   Larimer F.W., Malfatti S.A., Klotz M.G., Bottomley P.J., Arp D.J.,
RA   Hickey W.J.;
RT   "Genome sequence of the chemolithoautotrophic nitrite-oxidizing bacterium
RT   Nitrobacter winogradskyi Nb-255.";
RL   Appl. Environ. Microbiol. 72:2050-2063(2006).
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 + CO2 + ATP = (4R,5S)-
CC         dethiobiotin + ADP + phosphate + 3 H(+); 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; Evidence={ECO:0000255|HAMAP-
CC         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; CP000115; ABA05674.1; -; Genomic_DNA.
DR   RefSeq; WP_011315632.1; NC_007406.1.
DR   AlphaFoldDB; Q3SPW7; -.
DR   SMR; Q3SPW7; -.
DR   STRING; 323098.Nwi_2420; -.
DR   KEGG; nwi:Nwi_2420; -.
DR   eggNOG; COG0132; Bacteria.
DR   HOGENOM; CLU_072551_2_0_5; -.
DR   OrthoDB; 9802097at2; -.
DR   UniPathway; UPA00078; UER00161.
DR   Proteomes; UP000002531; Chromosome.
DR   GO; GO:0005829; C:cytosol; IEA:TreeGrafter.
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   CDD; cd03109; DTBS; 1.
DR   Gene3D; 3.40.50.300; P-loop containing nucleotide triphosphate hydrolases; 1.
DR   HAMAP; MF_00336; BioD; 1.
DR   InterPro; IPR004472; DTB_synth_BioD.
DR   InterPro; IPR027417; P-loop_NTPase.
DR   NCBIfam; TIGR00347; bioD; 1.
DR   PANTHER; PTHR43210:SF2; ATP-DEPENDENT DETHIOBIOTIN SYNTHETASE BIOD 2; 1.
DR   PANTHER; PTHR43210; DETHIOBIOTIN SYNTHETASE; 1.
DR   Pfam; PF13500; AAA_26; 1.
DR   PIRSF; PIRSF006755; DTB_synth; 1.
DR   SUPFAM; SSF52540; P-loop containing nucleoside triphosphate hydrolases; 1.
PE   3: Inferred from homology;
KW   ATP-binding; Biotin biosynthesis; Cytoplasm; Ligase; Magnesium;
KW   Metal-binding; Nucleotide-binding; Reference proteome.
FT   CHAIN           1..213
FT                   /note="ATP-dependent dethiobiotin synthetase BioD"
FT                   /id="PRO_0000302536"
FT   ACT_SITE        33
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT   BINDING         13..18
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT   BINDING         17
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT   BINDING         37
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT   BINDING         100..103
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT   BINDING         100
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
SQ   SEQUENCE   213 AA;  23168 MW;  759B2A14F34EA687 CRC64;
     MSARIVVSGT DTGVGKTVFS AALAGALDGY YWKPVQSGLD EETDSQTVMR LSGLGAERVW
     PEAYRLRTPV SPHLAAELDG VTIDHRALEA PHTDRPLVIE GAGGLLVPLT RDVTYLDLMA
     RWRLPVVLCA RTALGTINHS LLSIEALRAR DVAILGVSFI GEENVETEGI IIDMGRVKRL
     GRLSYVTPLT RATLRQAFAD GFDIGDFVKE RAR
//