ID   BIOD_NOVAD              Reviewed;         206 AA.
AC   Q2GAF9;
DT   05-FEB-2008, integrated into UniProtKB/Swiss-Prot.
DT   21-MAR-2006, sequence version 1.
DT   03-AUG-2022, entry version 87.
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=Saro_0717;
OS   Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG
OS   56034 / CIP 105152 / NBRC 16084 / F199).
OC   Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales;
OC   Sphingomonadaceae; Novosphingobium.
OX   NCBI_TaxID=279238;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 /
RC   F199;
RG   US DOE Joint Genome Institute;
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T.,
RA   Hammon N., Israni S., Pitluck S., Chain P., Malfatti S., Shin M.,
RA   Vergez L., Schmutz J., Larimer F., Land M., Kyrpides N., Ivanova N.,
RA   Fredrickson J., Balkwill D., Romine M.F., Richardson P.;
RT   "Complete sequence of Novosphingobium aromaticivorans DSM 12444.";
RL   Submitted (JAN-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; CP000248; ABD25164.1; -; Genomic_DNA.
DR   RefSeq; WP_011444378.1; NC_007794.1.
DR   AlphaFoldDB; Q2GAF9; -.
DR   SMR; Q2GAF9; -.
DR   STRING; 279238.Saro_0717; -.
DR   EnsemblBacteria; ABD25164; ABD25164; Saro_0717.
DR   KEGG; nar:Saro_0717; -.
DR   eggNOG; COG0132; Bacteria.
DR   HOGENOM; CLU_072551_2_0_5; -.
DR   OMA; SPHWAAE; -.
DR   OrthoDB; 1739932at2; -.
DR   UniPathway; UPA00078; UER00161.
DR   Proteomes; UP000009134; 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   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; Reference proteome.
FT   CHAIN           1..206
FT                   /note="ATP-dependent dethiobiotin synthetase BioD"
FT                   /id="PRO_1000059710"
FT   ACT_SITE        32
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         46
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT   BINDING         98..101
FT                   /ligand="ATP"
FT                   /ligand_id="ChEBI:CHEBI:30616"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
FT   BINDING         98
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00336"
SQ   SEQUENCE   206 AA;  21783 MW;  9259D5841A8FCEC1 CRC64;
     MTAFVVTGTD TGVGKTIFSA ALTGALNAHY WKPVQAGLED GADRDHVARL AGVPASHVLP
     ESYRLNTPCS PHRAAELDGV VLDLARIALP DVRPLVVEGA GGALVPVTRN TTYADVFAWW
     NLPVVIVART GLGTINHSLL TIEALRARGV PIHGVAFVGD AVEDSEATIC AMGEVRRLGR
     LPMLGQLDRP ALAQAFAEGF RVEDFA