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<entry dataset="Swiss-Prot" created="2002-10-25" modified="2026-01-28" version="111" xmlns="http://uniprot.org/uniprot">
  <accession>Q8U8T9</accession>
  <name>BIOD_AGRFC</name>
  <protein>
    <recommendedName>
      <fullName evidence="1">ATP-dependent dethiobiotin synthetase BioD</fullName>
      <ecNumber evidence="1">6.3.3.3</ecNumber>
    </recommendedName>
    <alternativeName>
      <fullName evidence="1">DTB synthetase</fullName>
      <shortName evidence="1">DTBS</shortName>
    </alternativeName>
    <alternativeName>
      <fullName evidence="1">Dethiobiotin synthase</fullName>
    </alternativeName>
  </protein>
  <gene>
    <name evidence="1" type="primary">bioD</name>
    <name type="ordered locus">Atu3999</name>
    <name type="ORF">AGR_L_1705</name>
  </gene>
  <organism>
    <name type="scientific">Agrobacterium fabrum (strain C58 / ATCC 33970)</name>
    <name type="common">Agrobacterium tumefaciens (strain C58)</name>
    <dbReference type="NCBI Taxonomy" id="176299"/>
    <lineage>
      <taxon>Bacteria</taxon>
      <taxon>Pseudomonadati</taxon>
      <taxon>Pseudomonadota</taxon>
      <taxon>Alphaproteobacteria</taxon>
      <taxon>Hyphomicrobiales</taxon>
      <taxon>Rhizobiaceae</taxon>
      <taxon>Rhizobium/Agrobacterium group</taxon>
      <taxon>Agrobacterium</taxon>
      <taxon>Agrobacterium tumefaciens complex</taxon>
    </lineage>
  </organism>
  <reference key="1">
    <citation type="journal article" date="2001" name="Science" volume="294" first="2317" last="2323">
      <title>The genome of the natural genetic engineer Agrobacterium tumefaciens C58.</title>
      <authorList>
        <person name="Wood D.W."/>
        <person name="Setubal J.C."/>
        <person name="Kaul R."/>
        <person name="Monks D.E."/>
        <person name="Kitajima J.P."/>
        <person name="Okura V.K."/>
        <person name="Zhou Y."/>
        <person name="Chen L."/>
        <person name="Wood G.E."/>
        <person name="Almeida N.F. Jr."/>
        <person name="Woo L."/>
        <person name="Chen Y."/>
        <person name="Paulsen I.T."/>
        <person name="Eisen J.A."/>
        <person name="Karp P.D."/>
        <person name="Bovee D. Sr."/>
        <person name="Chapman P."/>
        <person name="Clendenning J."/>
        <person name="Deatherage G."/>
        <person name="Gillet W."/>
        <person name="Grant C."/>
        <person name="Kutyavin T."/>
        <person name="Levy R."/>
        <person name="Li M.-J."/>
        <person name="McClelland E."/>
        <person name="Palmieri A."/>
        <person name="Raymond C."/>
        <person name="Rouse G."/>
        <person name="Saenphimmachak C."/>
        <person name="Wu Z."/>
        <person name="Romero P."/>
        <person name="Gordon D."/>
        <person name="Zhang S."/>
        <person name="Yoo H."/>
        <person name="Tao Y."/>
        <person name="Biddle P."/>
        <person name="Jung M."/>
        <person name="Krespan W."/>
        <person name="Perry M."/>
        <person name="Gordon-Kamm B."/>
        <person name="Liao L."/>
        <person name="Kim S."/>
        <person name="Hendrick C."/>
        <person name="Zhao Z.-Y."/>
        <person name="Dolan M."/>
        <person name="Chumley F."/>
        <person name="Tingey S.V."/>
        <person name="Tomb J.-F."/>
        <person name="Gordon M.P."/>
        <person name="Olson M.V."/>
        <person name="Nester E.W."/>
      </authorList>
      <dbReference type="PubMed" id="11743193"/>
      <dbReference type="DOI" id="10.1126/science.1066804"/>
    </citation>
    <scope>NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]</scope>
    <source>
      <strain>C58 / ATCC 33970</strain>
    </source>
  </reference>
  <reference key="2">
    <citation type="journal article" date="2001" name="Science" volume="294" first="2323" last="2328">
      <title>Genome sequence of the plant pathogen and biotechnology agent Agrobacterium tumefaciens C58.</title>
      <authorList>
        <person name="Goodner B."/>
        <person name="Hinkle G."/>
        <person name="Gattung S."/>
        <person name="Miller N."/>
        <person name="Blanchard M."/>
        <person name="Qurollo B."/>
        <person name="Goldman B.S."/>
        <person name="Cao Y."/>
        <person name="Askenazi M."/>
        <person name="Halling C."/>
        <person name="Mullin L."/>
        <person name="Houmiel K."/>
        <person name="Gordon J."/>
        <person name="Vaudin M."/>
        <person name="Iartchouk O."/>
        <person name="Epp A."/>
        <person name="Liu F."/>
        <person name="Wollam C."/>
        <person name="Allinger M."/>
        <person name="Doughty D."/>
        <person name="Scott C."/>
        <person name="Lappas C."/>
        <person name="Markelz B."/>
        <person name="Flanagan C."/>
        <person name="Crowell C."/>
        <person name="Gurson J."/>
        <person name="Lomo C."/>
        <person name="Sear C."/>
        <person name="Strub G."/>
        <person name="Cielo C."/>
        <person name="Slater S."/>
      </authorList>
      <dbReference type="PubMed" id="11743194"/>
      <dbReference type="DOI" id="10.1126/science.1066803"/>
    </citation>
    <scope>NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]</scope>
    <source>
      <strain>C58 / ATCC 33970</strain>
    </source>
  </reference>
  <comment type="function">
    <text evidence="1">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="1">
      <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="1">
      <name>Mg(2+)</name>
      <dbReference type="ChEBI" id="CHEBI:18420"/>
    </cofactor>
  </comment>
  <comment type="pathway">
    <text evidence="1">Cofactor biosynthesis; biotin biosynthesis; biotin from 7,8-diaminononanoate: step 1/2.</text>
  </comment>
  <comment type="subunit">
    <text evidence="1">Homodimer.</text>
  </comment>
  <comment type="subcellular location">
    <subcellularLocation>
      <location evidence="1">Cytoplasm</location>
    </subcellularLocation>
  </comment>
  <comment type="similarity">
    <text evidence="1">Belongs to the dethiobiotin synthetase family.</text>
  </comment>
  <dbReference type="EC" id="6.3.3.3" evidence="1"/>
  <dbReference type="EMBL" id="AE007870">
    <property type="protein sequence ID" value="AAK89426.1"/>
    <property type="molecule type" value="Genomic_DNA"/>
  </dbReference>
  <dbReference type="PIR" id="AC3048">
    <property type="entry name" value="AC3048"/>
  </dbReference>
  <dbReference type="PIR" id="H98237">
    <property type="entry name" value="H98237"/>
  </dbReference>
  <dbReference type="RefSeq" id="WP_010973493.1">
    <property type="nucleotide sequence ID" value="NC_003063.2"/>
  </dbReference>
  <dbReference type="AlphaFoldDB" id="Q8U8T9"/>
  <dbReference type="SMR" id="Q8U8T9"/>
  <dbReference type="STRING" id="176299.Atu3999"/>
  <dbReference type="EnsemblBacteria" id="AAK89426">
    <property type="protein sequence ID" value="AAK89426"/>
    <property type="gene ID" value="Atu3999"/>
  </dbReference>
  <dbReference type="GeneID" id="1135873"/>
  <dbReference type="KEGG" id="atu:Atu3999"/>
  <dbReference type="PATRIC" id="fig|176299.10.peg.3818"/>
  <dbReference type="eggNOG" id="COG0132">
    <property type="taxonomic scope" value="Bacteria"/>
  </dbReference>
  <dbReference type="HOGENOM" id="CLU_072551_2_0_5"/>
  <dbReference type="OrthoDB" id="9802097at2"/>
  <dbReference type="PhylomeDB" id="Q8U8T9"/>
  <dbReference type="BioCyc" id="AGRO:ATU3999-MONOMER"/>
  <dbReference type="UniPathway" id="UPA00078">
    <property type="reaction ID" value="UER00161"/>
  </dbReference>
  <dbReference type="Proteomes" id="UP000000813">
    <property type="component" value="Chromosome linear"/>
  </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: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="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:SF2">
    <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 id="KW-0067">ATP-binding</keyword>
  <keyword id="KW-0093">Biotin biosynthesis</keyword>
  <keyword id="KW-0963">Cytoplasm</keyword>
  <keyword id="KW-0436">Ligase</keyword>
  <keyword id="KW-0460">Magnesium</keyword>
  <keyword id="KW-0479">Metal-binding</keyword>
  <keyword id="KW-0547">Nucleotide-binding</keyword>
  <keyword id="KW-1185">Reference proteome</keyword>
  <feature type="chain" id="PRO_0000187944" description="ATP-dependent dethiobiotin synthetase BioD">
    <location>
      <begin position="1"/>
      <end position="212"/>
    </location>
  </feature>
  <feature type="active site" evidence="1">
    <location>
      <position position="33"/>
    </location>
  </feature>
  <feature type="binding site" evidence="1">
    <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="1">
    <location>
      <position position="17"/>
    </location>
    <ligand>
      <name>Mg(2+)</name>
      <dbReference type="ChEBI" id="CHEBI:18420"/>
    </ligand>
  </feature>
  <feature type="binding site" evidence="1">
    <location>
      <position position="37"/>
    </location>
    <ligand>
      <name>substrate</name>
    </ligand>
  </feature>
  <feature type="binding site" evidence="1">
    <location>
      <begin position="100"/>
      <end position="103"/>
    </location>
    <ligand>
      <name>ATP</name>
      <dbReference type="ChEBI" id="CHEBI:30616"/>
    </ligand>
  </feature>
  <feature type="binding site" evidence="1">
    <location>
      <position position="100"/>
    </location>
    <ligand>
      <name>Mg(2+)</name>
      <dbReference type="ChEBI" id="CHEBI:18420"/>
    </ligand>
  </feature>
  <feature type="binding site" evidence="1">
    <location>
      <begin position="184"/>
      <end position="186"/>
    </location>
    <ligand>
      <name>ATP</name>
      <dbReference type="ChEBI" id="CHEBI:30616"/>
    </ligand>
  </feature>
  <evidence type="ECO:0000255" key="1">
    <source>
      <dbReference type="HAMAP-Rule" id="MF_00336"/>
    </source>
  </evidence>
  <sequence length="212" mass="23115" checksum="050A562783F86AD0" modified="2002-06-01" version="1">MSLRFVISGTDTGIGKTVFAAALTHALEAHYWKPVQSGLEEETDSQTVARLAGASHARILPEAYRLKTPASPHLSARLDNVSIDPARLLPPRPDGPLVIEGAGGLLVPLTDRLLFADIFALWQIPLILCARTALGTINHTLLSLEALRHRAIPVQGVVFIGDEDRENERVITDIGAVRRLGRLPRLPELTPEALHQAFAQHFNLADFLEVPA</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>