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<entry dataset="Swiss-Prot" created="2008-01-15" modified="2026-09-02" version="107" xmlns="http://uniprot.org/uniprot">
  <accession>Q3K1T9</accession>
  <name>DDL_STRA1</name>
  <protein>
    <recommendedName>
      <fullName evidence="2">D-alanine--D-alanine ligase</fullName>
      <ecNumber evidence="2">6.3.2.4</ecNumber>
    </recommendedName>
    <alternativeName>
      <fullName evidence="2">D-Ala-D-Ala ligase</fullName>
    </alternativeName>
    <alternativeName>
      <fullName evidence="2">D-alanylalanine synthetase</fullName>
    </alternativeName>
  </protein>
  <gene>
    <name evidence="2" type="primary">ddl</name>
    <name type="ordered locus">SAK_0892</name>
  </gene>
  <organism>
    <name type="scientific">Streptococcus agalactiae serotype Ia (strain ATCC 27591 / A909 / CDC SS700)</name>
    <dbReference type="NCBI Taxonomy" id="205921"/>
    <lineage>
      <taxon>Bacteria</taxon>
      <taxon>Bacillati</taxon>
      <taxon>Bacillota</taxon>
      <taxon>Bacilli</taxon>
      <taxon>Lactobacillales</taxon>
      <taxon>Streptococcaceae</taxon>
      <taxon>Streptococcus</taxon>
    </lineage>
  </organism>
  <reference key="1">
    <citation type="journal article" date="2005" name="Proc. Natl. Acad. Sci. U.S.A." volume="102" first="13950" last="13955">
      <title>Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial 'pan-genome'.</title>
      <authorList>
        <person name="Tettelin H."/>
        <person name="Masignani V."/>
        <person name="Cieslewicz M.J."/>
        <person name="Donati C."/>
        <person name="Medini D."/>
        <person name="Ward N.L."/>
        <person name="Angiuoli S.V."/>
        <person name="Crabtree J."/>
        <person name="Jones A.L."/>
        <person name="Durkin A.S."/>
        <person name="DeBoy R.T."/>
        <person name="Davidsen T.M."/>
        <person name="Mora M."/>
        <person name="Scarselli M."/>
        <person name="Margarit y Ros I."/>
        <person name="Peterson J.D."/>
        <person name="Hauser C.R."/>
        <person name="Sundaram J.P."/>
        <person name="Nelson W.C."/>
        <person name="Madupu R."/>
        <person name="Brinkac L.M."/>
        <person name="Dodson R.J."/>
        <person name="Rosovitz M.J."/>
        <person name="Sullivan S.A."/>
        <person name="Daugherty S.C."/>
        <person name="Haft D.H."/>
        <person name="Selengut J."/>
        <person name="Gwinn M.L."/>
        <person name="Zhou L."/>
        <person name="Zafar N."/>
        <person name="Khouri H."/>
        <person name="Radune D."/>
        <person name="Dimitrov G."/>
        <person name="Watkins K."/>
        <person name="O'Connor K.J."/>
        <person name="Smith S."/>
        <person name="Utterback T.R."/>
        <person name="White O."/>
        <person name="Rubens C.E."/>
        <person name="Grandi G."/>
        <person name="Madoff L.C."/>
        <person name="Kasper D.L."/>
        <person name="Telford J.L."/>
        <person name="Wessels M.R."/>
        <person name="Rappuoli R."/>
        <person name="Fraser C.M."/>
      </authorList>
      <dbReference type="PubMed" id="16172379"/>
      <dbReference type="DOI" id="10.1073/pnas.0506758102"/>
    </citation>
    <scope>NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]</scope>
    <source>
      <strain>ATCC 27591 / A909 / CDC SS700</strain>
    </source>
  </reference>
  <comment type="function">
    <text evidence="2">Cell wall formation.</text>
  </comment>
  <comment type="catalytic activity">
    <reaction evidence="2">
      <text>2 D-alanine + ATP = D-alanyl-D-alanine + ADP + phosphate + H(+)</text>
      <dbReference type="Rhea" id="RHEA:11224"/>
      <dbReference type="ChEBI" id="CHEBI:15378"/>
      <dbReference type="ChEBI" id="CHEBI:30616"/>
      <dbReference type="ChEBI" id="CHEBI:43474"/>
      <dbReference type="ChEBI" id="CHEBI:57416"/>
      <dbReference type="ChEBI" id="CHEBI:57822"/>
      <dbReference type="ChEBI" id="CHEBI:456216"/>
      <dbReference type="EC" id="6.3.2.4"/>
    </reaction>
  </comment>
  <comment type="cofactor">
    <cofactor evidence="1">
      <name>Mg(2+)</name>
      <dbReference type="ChEBI" id="CHEBI:18420"/>
    </cofactor>
    <cofactor evidence="1">
      <name>Mn(2+)</name>
      <dbReference type="ChEBI" id="CHEBI:29035"/>
    </cofactor>
    <text evidence="1">Binds 2 magnesium or manganese ions per subunit.</text>
  </comment>
  <comment type="pathway">
    <text evidence="2">Cell wall biogenesis; peptidoglycan biosynthesis.</text>
  </comment>
  <comment type="subcellular location">
    <subcellularLocation>
      <location evidence="2">Cytoplasm</location>
    </subcellularLocation>
  </comment>
  <comment type="similarity">
    <text evidence="2">Belongs to the D-alanine--D-alanine ligase family.</text>
  </comment>
  <dbReference type="EC" id="6.3.2.4" evidence="2"/>
  <dbReference type="EMBL" id="CP000114">
    <property type="protein sequence ID" value="ABA45511.1"/>
    <property type="molecule type" value="Genomic_DNA"/>
  </dbReference>
  <dbReference type="RefSeq" id="WP_000032513.1">
    <property type="nucleotide sequence ID" value="NC_007432.1"/>
  </dbReference>
  <dbReference type="AlphaFoldDB" id="Q3K1T9"/>
  <dbReference type="SMR" id="Q3K1T9"/>
  <dbReference type="GeneID" id="66885719"/>
  <dbReference type="KEGG" id="sak:SAK_0892"/>
  <dbReference type="HOGENOM" id="CLU_039268_0_0_9"/>
  <dbReference type="UniPathway" id="UPA00219"/>
  <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="InterPro"/>
  </dbReference>
  <dbReference type="GO" id="GO:0008716">
    <property type="term" value="F:D-alanine-D-alanine ligase activity"/>
    <property type="evidence" value="ECO:0000501"/>
    <property type="project" value="UniProtKB-UniRule"/>
  </dbReference>
  <dbReference type="GO" id="GO:0046872">
    <property type="term" value="F:metal ion binding"/>
    <property type="evidence" value="ECO:0000501"/>
    <property type="project" value="InterPro"/>
  </dbReference>
  <dbReference type="GO" id="GO:0009252">
    <property type="term" value="P:peptidoglycan biosynthetic process"/>
    <property type="evidence" value="ECO:0000501"/>
    <property type="project" value="UniProtKB-UniRule"/>
  </dbReference>
  <dbReference type="FunFam" id="3.30.1490.20:FF:000007">
    <property type="entry name" value="D-alanine--D-alanine ligase"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="FunFam" id="3.30.470.20:FF:000008">
    <property type="entry name" value="D-alanine--D-alanine ligase"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="Gene3D" id="3.40.50.20">
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="Gene3D" id="3.30.1490.20">
    <property type="entry name" value="ATP-grasp fold, A domain"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="Gene3D" id="3.30.470.20">
    <property type="entry name" value="ATP-grasp fold, B domain"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="HAMAP" id="MF_00047">
    <property type="entry name" value="Dala_Dala_lig"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="InterPro" id="IPR011761">
    <property type="entry name" value="ATP-grasp"/>
  </dbReference>
  <dbReference type="InterPro" id="IPR013815">
    <property type="entry name" value="ATP_grasp_subdomain_1"/>
  </dbReference>
  <dbReference type="InterPro" id="IPR000291">
    <property type="entry name" value="D-Ala_lig_Van_CS"/>
  </dbReference>
  <dbReference type="InterPro" id="IPR005905">
    <property type="entry name" value="D_ala_D_ala"/>
  </dbReference>
  <dbReference type="InterPro" id="IPR011095">
    <property type="entry name" value="Dala_Dala_lig_C"/>
  </dbReference>
  <dbReference type="InterPro" id="IPR011127">
    <property type="entry name" value="Dala_Dala_lig_N"/>
  </dbReference>
  <dbReference type="InterPro" id="IPR016185">
    <property type="entry name" value="PreATP-grasp_dom_sf"/>
  </dbReference>
  <dbReference type="NCBIfam" id="TIGR01205">
    <property type="entry name" value="D_ala_D_alaTIGR"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="NCBIfam" id="NF002528">
    <property type="entry name" value="PRK01966.1-4"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="NCBIfam" id="NF002529">
    <property type="entry name" value="PRK01966.1-5"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="PANTHER" id="PTHR23132">
    <property type="entry name" value="D-ALANINE--D-ALANINE LIGASE"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="PANTHER" id="PTHR23132:SF25">
    <property type="entry name" value="D-ALANINE--D-ALANINE LIGASE A"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="Pfam" id="PF07478">
    <property type="entry name" value="Dala_Dala_lig_C"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="Pfam" id="PF01820">
    <property type="entry name" value="Dala_Dala_lig_N"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="PIRSF" id="PIRSF039102">
    <property type="entry name" value="Ddl/VanB"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="SUPFAM" id="SSF56059">
    <property type="entry name" value="Glutathione synthetase ATP-binding domain-like"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="SUPFAM" id="SSF52440">
    <property type="entry name" value="PreATP-grasp domain"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="PROSITE" id="PS50975">
    <property type="entry name" value="ATP_GRASP"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="PROSITE" id="PS00843">
    <property type="entry name" value="DALA_DALA_LIGASE_1"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="PROSITE" id="PS00844">
    <property type="entry name" value="DALA_DALA_LIGASE_2"/>
    <property type="match status" value="1"/>
  </dbReference>
  <proteinExistence type="inferred from homology"/>
  <keyword id="KW-0067">ATP-binding</keyword>
  <keyword id="KW-0133">Cell shape</keyword>
  <keyword id="KW-0961">Cell wall biogenesis/degradation</keyword>
  <keyword id="KW-0963">Cytoplasm</keyword>
  <keyword id="KW-0436">Ligase</keyword>
  <keyword id="KW-0460">Magnesium</keyword>
  <keyword id="KW-0464">Manganese</keyword>
  <keyword id="KW-0479">Metal-binding</keyword>
  <keyword id="KW-0547">Nucleotide-binding</keyword>
  <keyword id="KW-0573">Peptidoglycan synthesis</keyword>
  <feature type="chain" id="PRO_1000030498" description="D-alanine--D-alanine ligase">
    <location>
      <begin position="1"/>
      <end position="348"/>
    </location>
  </feature>
  <feature type="domain" description="ATP-grasp" evidence="2">
    <location>
      <begin position="132"/>
      <end position="334"/>
    </location>
  </feature>
  <feature type="binding site" evidence="2">
    <location>
      <begin position="162"/>
      <end position="217"/>
    </location>
    <ligand>
      <name>ATP</name>
      <dbReference type="ChEBI" id="CHEBI:30616"/>
    </ligand>
  </feature>
  <feature type="binding site" evidence="2">
    <location>
      <position position="288"/>
    </location>
    <ligand>
      <name>Mg(2+)</name>
      <dbReference type="ChEBI" id="CHEBI:18420"/>
      <label>1</label>
    </ligand>
  </feature>
  <feature type="binding site" evidence="2">
    <location>
      <position position="301"/>
    </location>
    <ligand>
      <name>Mg(2+)</name>
      <dbReference type="ChEBI" id="CHEBI:18420"/>
      <label>1</label>
    </ligand>
  </feature>
  <feature type="binding site" evidence="2">
    <location>
      <position position="301"/>
    </location>
    <ligand>
      <name>Mg(2+)</name>
      <dbReference type="ChEBI" id="CHEBI:18420"/>
      <label>2</label>
    </ligand>
  </feature>
  <feature type="binding site" evidence="2">
    <location>
      <position position="303"/>
    </location>
    <ligand>
      <name>Mg(2+)</name>
      <dbReference type="ChEBI" id="CHEBI:18420"/>
      <label>2</label>
    </ligand>
  </feature>
  <evidence type="ECO:0000250" key="1"/>
  <evidence type="ECO:0000255" key="2">
    <source>
      <dbReference type="HAMAP-Rule" id="MF_00047"/>
    </source>
  </evidence>
  <sequence length="348" mass="39068" checksum="619B27BA8267F7E1" modified="2005-11-08" version="1">MSKETLILLYGGRSAEREVSVLSAESVMRAINYDKFFVKTYFITQVGQFIKTQEFDEMPSSDEKLMTNQTVDLDKMVRPSDIYDDNAIVFPVLHGPMGEDGSIQGFLEVLRMPYVGTNILSSSVAMDKITTKQVLATVGVPQVAYQTYFEGDDLEHAIKLSLETLSFPIFVKPANMGSSVGISKATDESSLRSAIDLALKYDSRILIEQGVTAREIEVGILGNNDVKTTFPGEVVKDVDFYDYDAKYIDNKITMDIPAKVDEATMEAMRQYASKAFKAIGACGLSRCDFFLTKDGQIFLNELNTMPGFTQWSMYPLLWENMGLTYSDLIEKLVMLAKEMFEKRESHLI</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>