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<entry dataset="TrEMBL" created="2003-12-15" modified="2025-10-08" version="130" xmlns="http://uniprot.org/uniprot">
  <accession>Q7N4T9</accession>
  <name>Q7N4T9_PHOLL</name>
  <protein>
    <recommendedName>
      <fullName evidence="8">ATP-dependent dethiobiotin synthetase BioD</fullName>
      <ecNumber evidence="8">6.3.3.3</ecNumber>
    </recommendedName>
    <alternativeName>
      <fullName evidence="8">DTB synthetase</fullName>
      <shortName evidence="8">DTBS</shortName>
    </alternativeName>
    <alternativeName>
      <fullName evidence="8">Dethiobiotin synthase</fullName>
    </alternativeName>
  </protein>
  <gene>
    <name evidence="8" type="primary">bioD</name>
    <name evidence="9" type="ordered locus">plu2227</name>
  </gene>
  <organism evidence="9 10">
    <name type="scientific">Photorhabdus laumondii subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)</name>
    <name type="common">Photorhabdus luminescens subsp. laumondii</name>
    <dbReference type="NCBI Taxonomy" id="243265"/>
    <lineage>
      <taxon>Bacteria</taxon>
      <taxon>Pseudomonadati</taxon>
      <taxon>Pseudomonadota</taxon>
      <taxon>Gammaproteobacteria</taxon>
      <taxon>Enterobacterales</taxon>
      <taxon>Morganellaceae</taxon>
      <taxon>Photorhabdus</taxon>
    </lineage>
  </organism>
  <reference evidence="10" key="1">
    <citation type="journal article" date="2003" name="Nat. Biotechnol." volume="21" first="1307" last="1313">
      <title>The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens.</title>
      <authorList>
        <person name="Duchaud E."/>
        <person name="Rusniok C."/>
        <person name="Frangeul L."/>
        <person name="Buchrieser C."/>
        <person name="Givaudan A."/>
        <person name="Taourit S."/>
        <person name="Bocs S."/>
        <person name="Boursaux-Eude C."/>
        <person name="Chandler M."/>
        <person name="Charles J.-F."/>
        <person name="Dassa E."/>
        <person name="Derose R."/>
        <person name="Derzelle S."/>
        <person name="Freyssinet G."/>
        <person name="Gaudriault S."/>
        <person name="Medigue C."/>
        <person name="Lanois A."/>
        <person name="Powell K."/>
        <person name="Siguier P."/>
        <person name="Vincent R."/>
        <person name="Wingate V."/>
        <person name="Zouine M."/>
        <person name="Glaser P."/>
        <person name="Boemare N."/>
        <person name="Danchin A."/>
        <person name="Kunst F."/>
      </authorList>
      <dbReference type="PubMed" id="14528314"/>
      <dbReference type="DOI" id="10.1038/nbt886"/>
    </citation>
    <scope>NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]</scope>
    <source>
      <strain evidence="10">DSM 15139 / CIP 105565 / TT01</strain>
    </source>
  </reference>
  <comment type="function">
    <text evidence="8">Catalyzes a mechanistically unusual reaction, the ATP-dependent insertion of CO2 between the N7 and N8 nitrogen atoms of 7,8-diaminopelargonic acid (DAPA, also called 7,8-diammoniononanoate) to form a ureido ring.</text>
  </comment>
  <comment type="catalytic activity">
    <reaction evidence="8">
      <text>(7R,8S)-7,8-diammoniononanoate + CO2 + ATP = (4R,5S)-dethiobiotin + ADP + phosphate + 3 H(+)</text>
      <dbReference type="Rhea" id="RHEA:15805"/>
      <dbReference type="ChEBI" id="CHEBI:15378"/>
      <dbReference type="ChEBI" id="CHEBI:16526"/>
      <dbReference type="ChEBI" id="CHEBI:30616"/>
      <dbReference type="ChEBI" id="CHEBI:43474"/>
      <dbReference type="ChEBI" id="CHEBI:149469"/>
      <dbReference type="ChEBI" id="CHEBI:149473"/>
      <dbReference type="ChEBI" id="CHEBI:456216"/>
      <dbReference type="EC" id="6.3.3.3"/>
    </reaction>
  </comment>
  <comment type="cofactor">
    <cofactor evidence="8">
      <name>Mg(2+)</name>
      <dbReference type="ChEBI" id="CHEBI:18420"/>
    </cofactor>
  </comment>
  <comment type="pathway">
    <text evidence="8">Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 1/2.</text>
  </comment>
  <comment type="subunit">
    <text evidence="8">Homodimer.</text>
  </comment>
  <comment type="subcellular location">
    <subcellularLocation>
      <location evidence="8">Cytoplasm</location>
    </subcellularLocation>
  </comment>
  <comment type="similarity">
    <text evidence="8">Belongs to the dethiobiotin synthetase family.</text>
  </comment>
  <comment type="caution">
    <text evidence="8">Lacks conserved residue(s) required for the propagation of feature annotation.</text>
  </comment>
  <dbReference type="EC" id="6.3.3.3" evidence="8"/>
  <dbReference type="EMBL" id="BX571866">
    <property type="protein sequence ID" value="CAE14520.1"/>
    <property type="molecule type" value="Genomic_DNA"/>
  </dbReference>
  <dbReference type="RefSeq" id="WP_011146478.1">
    <property type="nucleotide sequence ID" value="NC_005126.1"/>
  </dbReference>
  <dbReference type="AlphaFoldDB" id="Q7N4T9"/>
  <dbReference type="STRING" id="243265.plu2227"/>
  <dbReference type="GeneID" id="48848502"/>
  <dbReference type="KEGG" id="plu:plu2227"/>
  <dbReference type="eggNOG" id="COG0132">
    <property type="taxonomic scope" value="Bacteria"/>
  </dbReference>
  <dbReference type="HOGENOM" id="CLU_072551_0_0_6"/>
  <dbReference type="OrthoDB" id="9802097at2"/>
  <dbReference type="UniPathway" id="UPA00078">
    <property type="reaction ID" value="UER00161"/>
  </dbReference>
  <dbReference type="Proteomes" id="UP000002514">
    <property type="component" value="Chromosome"/>
  </dbReference>
  <dbReference type="GO" id="GO:0005829">
    <property type="term" value="C:cytosol"/>
    <property type="evidence" value="ECO:0000501"/>
    <property type="project" value="TreeGrafter"/>
  </dbReference>
  <dbReference type="GO" id="GO:0005524">
    <property type="term" value="F:ATP binding"/>
    <property type="evidence" value="ECO:0000501"/>
    <property type="project" value="UniProtKB-UniRule"/>
  </dbReference>
  <dbReference type="GO" id="GO:0004141">
    <property type="term" value="F:dethiobiotin synthase activity"/>
    <property type="evidence" value="ECO:0000501"/>
    <property type="project" value="UniProtKB-UniRule"/>
  </dbReference>
  <dbReference type="GO" id="GO:0000287">
    <property type="term" value="F:magnesium ion binding"/>
    <property type="evidence" value="ECO:0000501"/>
    <property type="project" value="UniProtKB-UniRule"/>
  </dbReference>
  <dbReference type="GO" id="GO:0042803">
    <property type="term" value="F:protein homodimerization activity"/>
    <property type="evidence" value="ECO:0000501"/>
    <property type="project" value="UniProtKB-ARBA"/>
  </dbReference>
  <dbReference type="GO" id="GO:0009102">
    <property type="term" value="P:biotin biosynthetic process"/>
    <property type="evidence" value="ECO:0000501"/>
    <property type="project" value="UniProtKB-UniRule"/>
  </dbReference>
  <dbReference type="CDD" id="cd03109">
    <property type="entry name" value="DTBS"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="FunFam" id="3.40.50.300:FF:000292">
    <property type="entry name" value="ATP-dependent dethiobiotin synthetase BioD"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="Gene3D" id="3.40.50.300">
    <property type="entry name" value="P-loop containing nucleotide triphosphate hydrolases"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="HAMAP" id="MF_00336">
    <property type="entry name" value="BioD"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="InterPro" id="IPR004472">
    <property type="entry name" value="DTB_synth_BioD"/>
  </dbReference>
  <dbReference type="InterPro" id="IPR027417">
    <property type="entry name" value="P-loop_NTPase"/>
  </dbReference>
  <dbReference type="NCBIfam" id="TIGR00347">
    <property type="entry name" value="bioD"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="PANTHER" id="PTHR43210:SF4">
    <property type="entry name" value="ATP-DEPENDENT DETHIOBIOTIN SYNTHETASE BIOD 2"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="PANTHER" id="PTHR43210">
    <property type="entry name" value="DETHIOBIOTIN SYNTHETASE"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="Pfam" id="PF13500">
    <property type="entry name" value="AAA_26"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="PIRSF" id="PIRSF006755">
    <property type="entry name" value="DTB_synth"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="SUPFAM" id="SSF52540">
    <property type="entry name" value="P-loop containing nucleoside triphosphate hydrolases"/>
    <property type="match status" value="1"/>
  </dbReference>
  <proteinExistence type="inferred from homology"/>
  <keyword evidence="6 8" id="KW-0067">ATP-binding</keyword>
  <keyword evidence="5 8" id="KW-0093">Biotin biosynthesis</keyword>
  <keyword evidence="1 8" id="KW-0963">Cytoplasm</keyword>
  <keyword evidence="2 8" id="KW-0436">Ligase</keyword>
  <keyword evidence="7 8" id="KW-0460">Magnesium</keyword>
  <keyword evidence="3 8" id="KW-0479">Metal-binding</keyword>
  <keyword evidence="4 8" id="KW-0547">Nucleotide-binding</keyword>
  <keyword evidence="10" id="KW-1185">Reference proteome</keyword>
  <feature type="active site" evidence="8">
    <location>
      <position position="38"/>
    </location>
  </feature>
  <feature type="binding site" evidence="8">
    <location>
      <begin position="13"/>
      <end position="18"/>
    </location>
    <ligand>
      <name>ATP</name>
      <dbReference type="ChEBI" id="CHEBI:30616"/>
    </ligand>
  </feature>
  <feature type="binding site" evidence="8">
    <location>
      <position position="17"/>
    </location>
    <ligand>
      <name>Mg(2+)</name>
      <dbReference type="ChEBI" id="CHEBI:18420"/>
    </ligand>
  </feature>
  <feature type="binding site" evidence="8">
    <location>
      <position position="42"/>
    </location>
    <ligand>
      <name>substrate</name>
    </ligand>
  </feature>
  <feature type="binding site" evidence="8">
    <location>
      <position position="55"/>
    </location>
    <ligand>
      <name>ATP</name>
      <dbReference type="ChEBI" id="CHEBI:30616"/>
    </ligand>
  </feature>
  <feature type="binding site" evidence="8">
    <location>
      <position position="55"/>
    </location>
    <ligand>
      <name>Mg(2+)</name>
      <dbReference type="ChEBI" id="CHEBI:18420"/>
    </ligand>
  </feature>
  <feature type="binding site" evidence="8">
    <location>
      <begin position="109"/>
      <end position="112"/>
    </location>
    <ligand>
      <name>ATP</name>
      <dbReference type="ChEBI" id="CHEBI:30616"/>
    </ligand>
  </feature>
  <feature type="binding site" evidence="8">
    <location>
      <position position="109"/>
    </location>
    <ligand>
      <name>Mg(2+)</name>
      <dbReference type="ChEBI" id="CHEBI:18420"/>
    </ligand>
  </feature>
  <feature type="binding site" evidence="8">
    <location>
      <begin position="169"/>
      <end position="170"/>
    </location>
    <ligand>
      <name>ATP</name>
      <dbReference type="ChEBI" id="CHEBI:30616"/>
    </ligand>
  </feature>
  <feature type="binding site" evidence="8">
    <location>
      <begin position="198"/>
      <end position="200"/>
    </location>
    <ligand>
      <name>ATP</name>
      <dbReference type="ChEBI" id="CHEBI:30616"/>
    </ligand>
  </feature>
  <evidence type="ECO:0000256" key="1">
    <source>
      <dbReference type="ARBA" id="ARBA00022490"/>
    </source>
  </evidence>
  <evidence type="ECO:0000256" key="2">
    <source>
      <dbReference type="ARBA" id="ARBA00022598"/>
    </source>
  </evidence>
  <evidence type="ECO:0000256" key="3">
    <source>
      <dbReference type="ARBA" id="ARBA00022723"/>
    </source>
  </evidence>
  <evidence type="ECO:0000256" key="4">
    <source>
      <dbReference type="ARBA" id="ARBA00022741"/>
    </source>
  </evidence>
  <evidence type="ECO:0000256" key="5">
    <source>
      <dbReference type="ARBA" id="ARBA00022756"/>
    </source>
  </evidence>
  <evidence type="ECO:0000256" key="6">
    <source>
      <dbReference type="ARBA" id="ARBA00022840"/>
    </source>
  </evidence>
  <evidence type="ECO:0000256" key="7">
    <source>
      <dbReference type="ARBA" id="ARBA00022842"/>
    </source>
  </evidence>
  <evidence type="ECO:0000256" key="8">
    <source>
      <dbReference type="HAMAP-Rule" id="MF_00336"/>
    </source>
  </evidence>
  <evidence type="ECO:0000313" key="9">
    <source>
      <dbReference type="EMBL" id="CAE14520.1"/>
    </source>
  </evidence>
  <evidence type="ECO:0000313" key="10">
    <source>
      <dbReference type="Proteomes" id="UP000002514"/>
    </source>
  </evidence>
  <sequence length="235" mass="26329" checksum="887749F2B9126B9C" modified="2003-12-15" version="1">MLTRLFVTGTDTNIGKTIVTRALLQAFNRDGATAVGYKPIATEGYETEEGMRNRDGVILQKSSPVPLKYEEINPVIWKNSYCEGNQVDFEQMKKGLNNLSNKADRVIIEGNGGWRVLLDDETFYFDWVIQEKIPVILVVGIQPGCVNHSILTAQAIINDGLQLVGWVANRINPGLSHYTKVMDRLRRHINAPQLGEIPYILRPEEKDLSCYLDVATIFKQVGGSESEVGIESQYT</sequence>
</entry>
<copyright>
Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms Distributed under the Creative Commons Attribution (CC BY 4.0) License
</copyright>
</uniprot>