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<entry dataset="Swiss-Prot" created="2008-01-15" modified="2026-09-02" version="112" xmlns="http://uniprot.org/uniprot">
  <accession>Q0T9N4</accession>
  <name>EPMA_ECOL5</name>
  <protein>
    <recommendedName>
      <fullName evidence="1">Elongation factor P--(R)-beta-lysine ligase</fullName>
      <shortName evidence="1">EF-P--(R)-beta-lysine ligase</shortName>
      <ecNumber evidence="1">6.3.2.-</ecNumber>
    </recommendedName>
    <alternativeName>
      <fullName evidence="1">EF-P post-translational modification enzyme A</fullName>
    </alternativeName>
    <alternativeName>
      <fullName evidence="1">EF-P-lysine lysyltransferase</fullName>
    </alternativeName>
  </protein>
  <gene>
    <name evidence="1" type="primary">epmA</name>
    <name type="synonym">yjeA</name>
    <name type="ordered locus">ECP_4401</name>
  </gene>
  <organism>
    <name type="scientific">Escherichia coli O6:K15:H31 (strain 536 / UPEC)</name>
    <dbReference type="NCBI Taxonomy" id="362663"/>
    <lineage>
      <taxon>Bacteria</taxon>
      <taxon>Pseudomonadati</taxon>
      <taxon>Pseudomonadota</taxon>
      <taxon>Gammaproteobacteria</taxon>
      <taxon>Enterobacterales</taxon>
      <taxon>Enterobacteriaceae</taxon>
      <taxon>Escherichia</taxon>
    </lineage>
  </organism>
  <reference key="1">
    <citation type="journal article" date="2006" name="Mol. Microbiol." volume="61" first="584" last="595">
      <title>Role of pathogenicity island-associated integrases in the genome plasticity of uropathogenic Escherichia coli strain 536.</title>
      <authorList>
        <person name="Hochhut B."/>
        <person name="Wilde C."/>
        <person name="Balling G."/>
        <person name="Middendorf B."/>
        <person name="Dobrindt U."/>
        <person name="Brzuszkiewicz E."/>
        <person name="Gottschalk G."/>
        <person name="Carniel E."/>
        <person name="Hacker J."/>
      </authorList>
      <dbReference type="PubMed" id="16879640"/>
      <dbReference type="DOI" id="10.1111/j.1365-2958.2006.05255.x"/>
    </citation>
    <scope>NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]</scope>
    <source>
      <strain>536 / UPEC</strain>
    </source>
  </reference>
  <comment type="function">
    <text evidence="1">With EpmB is involved in the beta-lysylation step of the post-translational modification of translation elongation factor P (EF-P) on 'Lys-34'. Catalyzes the ATP-dependent activation of (R)-beta-lysine produced by EpmB, forming a lysyl-adenylate, from which the beta-lysyl moiety is then transferred to the epsilon-amino group of EF-P 'Lys-34'.</text>
  </comment>
  <comment type="catalytic activity">
    <reaction evidence="1">
      <text>D-beta-lysine + L-lysyl-[protein] + ATP = N(6)-((3R)-3,6-diaminohexanoyl)-L-lysyl-[protein] + AMP + diphosphate + H(+)</text>
      <dbReference type="Rhea" id="RHEA:83435"/>
      <dbReference type="Rhea" id="RHEA-COMP:9752"/>
      <dbReference type="Rhea" id="RHEA-COMP:20131"/>
      <dbReference type="ChEBI" id="CHEBI:15378"/>
      <dbReference type="ChEBI" id="CHEBI:29969"/>
      <dbReference type="ChEBI" id="CHEBI:30616"/>
      <dbReference type="ChEBI" id="CHEBI:33019"/>
      <dbReference type="ChEBI" id="CHEBI:84138"/>
      <dbReference type="ChEBI" id="CHEBI:156053"/>
      <dbReference type="ChEBI" id="CHEBI:456215"/>
    </reaction>
    <physiologicalReaction direction="left-to-right" evidence="1">
      <dbReference type="Rhea" id="RHEA:83436"/>
    </physiologicalReaction>
  </comment>
  <comment type="subunit">
    <text evidence="1">Homodimer.</text>
  </comment>
  <comment type="similarity">
    <text evidence="1">Belongs to the class-II aminoacyl-tRNA synthetase family. EpmA subfamily.</text>
  </comment>
  <dbReference type="EC" id="6.3.2.-" evidence="1"/>
  <dbReference type="EMBL" id="CP000247">
    <property type="protein sequence ID" value="ABG72345.1"/>
    <property type="molecule type" value="Genomic_DNA"/>
  </dbReference>
  <dbReference type="RefSeq" id="WP_000004771.1">
    <property type="nucleotide sequence ID" value="NC_008253.1"/>
  </dbReference>
  <dbReference type="AlphaFoldDB" id="Q0T9N4"/>
  <dbReference type="SMR" id="Q0T9N4"/>
  <dbReference type="GeneID" id="93777667"/>
  <dbReference type="KEGG" id="ecp:ECP_4401"/>
  <dbReference type="HOGENOM" id="CLU_008255_1_1_6"/>
  <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:0016880">
    <property type="term" value="F:acid-ammonia (or amide) ligase activity"/>
    <property type="evidence" value="ECO:0000501"/>
    <property type="project" value="UniProtKB-UniRule"/>
  </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:0004824">
    <property type="term" value="F:lysine-tRNA ligase activity"/>
    <property type="evidence" value="ECO:0000501"/>
    <property type="project" value="InterPro"/>
  </dbReference>
  <dbReference type="GO" id="GO:0052868">
    <property type="term" value="F:protein-lysine lysyltransferase activity"/>
    <property type="evidence" value="ECO:0000501"/>
    <property type="project" value="RHEA"/>
  </dbReference>
  <dbReference type="GO" id="GO:0000049">
    <property type="term" value="F:tRNA binding"/>
    <property type="evidence" value="ECO:0000501"/>
    <property type="project" value="TreeGrafter"/>
  </dbReference>
  <dbReference type="GO" id="GO:0006430">
    <property type="term" value="P:lysyl-tRNA aminoacylation"/>
    <property type="evidence" value="ECO:0000501"/>
    <property type="project" value="InterPro"/>
  </dbReference>
  <dbReference type="FunFam" id="3.30.930.10:FF:000017">
    <property type="entry name" value="Elongation factor P--(R)-beta-lysine ligase"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="Gene3D" id="3.30.930.10">
    <property type="entry name" value="Bira Bifunctional Protein, Domain 2"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="HAMAP" id="MF_00174">
    <property type="entry name" value="EF_P_modif_A"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="InterPro" id="IPR004364">
    <property type="entry name" value="Aa-tRNA-synt_II"/>
  </dbReference>
  <dbReference type="InterPro" id="IPR006195">
    <property type="entry name" value="aa-tRNA-synth_II"/>
  </dbReference>
  <dbReference type="InterPro" id="IPR045864">
    <property type="entry name" value="aa-tRNA-synth_II/BPL/LPL"/>
  </dbReference>
  <dbReference type="InterPro" id="IPR004525">
    <property type="entry name" value="EpmA"/>
  </dbReference>
  <dbReference type="InterPro" id="IPR018149">
    <property type="entry name" value="Lys-tRNA-synth_II_C"/>
  </dbReference>
  <dbReference type="NCBIfam" id="TIGR00462">
    <property type="entry name" value="genX"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="NCBIfam" id="NF006828">
    <property type="entry name" value="PRK09350.1"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="PANTHER" id="PTHR42918:SF6">
    <property type="entry name" value="ELONGATION FACTOR P--(R)-BETA-LYSINE LIGASE"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="PANTHER" id="PTHR42918">
    <property type="entry name" value="LYSYL-TRNA SYNTHETASE"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="Pfam" id="PF00152">
    <property type="entry name" value="tRNA-synt_2"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="PRINTS" id="PR00982">
    <property type="entry name" value="TRNASYNTHLYS"/>
  </dbReference>
  <dbReference type="SUPFAM" id="SSF55681">
    <property type="entry name" value="Class II aaRS and biotin synthetases"/>
    <property type="match status" value="1"/>
  </dbReference>
  <dbReference type="PROSITE" id="PS50862">
    <property type="entry name" value="AA_TRNA_LIGASE_II"/>
    <property type="match status" value="1"/>
  </dbReference>
  <proteinExistence type="inferred from homology"/>
  <keyword id="KW-0067">ATP-binding</keyword>
  <keyword id="KW-0436">Ligase</keyword>
  <keyword id="KW-0547">Nucleotide-binding</keyword>
  <feature type="chain" id="PRO_1000023620" description="Elongation factor P--(R)-beta-lysine ligase">
    <location>
      <begin position="1"/>
      <end position="325"/>
    </location>
  </feature>
  <feature type="binding site" evidence="1">
    <location>
      <begin position="76"/>
      <end position="78"/>
    </location>
    <ligand>
      <name>substrate</name>
    </ligand>
  </feature>
  <feature type="binding site" evidence="1">
    <location>
      <begin position="100"/>
      <end position="102"/>
    </location>
    <ligand>
      <name>ATP</name>
      <dbReference type="ChEBI" id="CHEBI:30616"/>
    </ligand>
  </feature>
  <feature type="binding site" evidence="1">
    <location>
      <position position="109"/>
    </location>
    <ligand>
      <name>ATP</name>
      <dbReference type="ChEBI" id="CHEBI:30616"/>
    </ligand>
  </feature>
  <feature type="binding site" evidence="1">
    <location>
      <position position="118"/>
    </location>
    <ligand>
      <name>substrate</name>
    </ligand>
  </feature>
  <feature type="binding site" evidence="1">
    <location>
      <begin position="244"/>
      <end position="245"/>
    </location>
    <ligand>
      <name>ATP</name>
      <dbReference type="ChEBI" id="CHEBI:30616"/>
    </ligand>
  </feature>
  <feature type="binding site" evidence="1">
    <location>
      <position position="251"/>
    </location>
    <ligand>
      <name>substrate</name>
    </ligand>
  </feature>
  <feature type="binding site" evidence="1">
    <location>
      <position position="300"/>
    </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_00174"/>
    </source>
  </evidence>
  <sequence length="325" mass="36976" checksum="F72B535CCA23E4CC" modified="2006-09-05" version="1">MSETASWQPSASIPNLLKRAAIMAEIRRFFADRGVLEVETPCMSQATVTDIHLVPFETRFVGPGHSQGMNLWLMTSPEYHMKRLLVAGCGPVFQLCRSFRNEEMGRYHNPEFTMLEWYRPHYDMYRLMNEVDDLLQQVLDCPAAESLSYQQAFLRYLEIDPLSADKTQLREVAAKLDLSNVADTEEDRDTLLQLLFTFGVEPNIGKEKPTFVYHFPASQASLAQISTEDHRVAERFEVYYKGIELANGFHELTDAREQQQRFEQDNRKRAARGLPQHPIDQNLIEALKVGMPDCSGVALGVDRLVMLALGAETLAEVIAFSVDRA</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>