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Protein

Elongation factor P--(R)-beta-lysine ligase

Gene

epmA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

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'. (R)-beta-lysine is 100-fold more efficient as a substrate than either (S)-beta-lysine or L-alpha-lysine. Cannot ligate lysine to any tRNA.UniRule annotation3 Publications

Caution

Was originally suggested to be a tRNA synthase, however its lack of an anticodon-binding domain made this highly unlikely.1 Publication

Kineticsi

kcat is 36 min(-1) for the amino acid activation reaction with (R)-beta-lysine as substrate.
  1. KM=213 µM for (R)-beta-lysine1 Publication
  2. KM=8600 µM for L-alpha-lysine1 Publication
  3. KM=6950 µM for (S)-beta-lysine1 Publication
  4. KM=206 µM for ATP1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei109ATP; via amide nitrogen and carbonyl oxygen1
    Binding sitei118Substrate1
    Binding sitei251Substrate1
    Binding sitei300ATP; via amide nitrogen1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi100 – 102ATP3
    Nucleotide bindingi244 – 245ATP2

    GO - Molecular functioni

    • ATP binding Source: UniProtKB-KW
    • lysine-tRNA ligase activity Source: InterPro
    • protein-lysine lysyltransferase activity Source: EcoCyc

    GO - Biological processi

    • lysyl-tRNA aminoacylation Source: InterPro
    • protein-lysine lysylation Source: EcoCyc
    • protein-N6-(L-lysyl)-L-lysine modification to protein-N6-(beta-lysyl)-L-lysine Source: EcoCyc

    Keywordsi

    Molecular functionLigase
    LigandATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11211-MONOMER
    MetaCyc:EG11211-MONOMER

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Elongation factor P--(R)-beta-lysine ligaseUniRule annotation (EC:6.3.1.-UniRule annotation)
    Short name:
    EF-P--(R)-beta-lysine ligaseUniRule annotation
    Alternative name(s):
    EF-P post-translational modification enzyme AUniRule annotation
    EF-P-lysine lysyltransferaseUniRule annotation
    GX
    Gene namesi
    Name:epmAUniRule annotation
    Synonyms:genX, poxA, yjeA
    Ordered Locus Names:b4155, JW4116
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11211 epmA

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: EcoCyc

    Pathology & Biotechi

    Disruption phenotypei

    Cells have a reduced pyruvate oxidase activity and a reduced growth rate. Cells lack CadA activity (lysine decarboxylase).3 Publications

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi50D → A: No effect on lysylation activity. 1 Publication1
    Mutagenesisi76S → A: Loss of catalytic activity. 1 Publication1
    Mutagenesisi100R → A: Loss of lysylation activity. 1 Publication1
    Mutagenesisi102E → A: No effect on lysylation activity. 1 Publication1
    Mutagenesisi103E → A: Loss of lysylation activity. 1 Publication1
    Mutagenesisi108H → A: Severe reduction in lysylation activity. 1 Publication1
    Mutagenesisi185E → A: Slight reduction in lysylation activity. 1 Publication1
    Mutagenesisi193Q → A: Slight reduction in lysylation activity. 1 Publication1
    Mutagenesisi244E → A: Loss of lysylation activity. 1 Publication1
    Mutagenesisi247N → A: Loss of lysylation activity. 1 Publication1
    Mutagenesisi298A → G: 96% increase in the affinity for L-alpha-lysine. 4-fold decrease in the catalytic efficiency of the (R)-beta-lysine activation reaction. 1 Publication1
    Mutagenesisi303R → A: Loss of lysylation activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001527191 – 325Elongation factor P--(R)-beta-lysine ligaseAdd BLAST325

    Proteomic databases

    PaxDbiP0A8N7
    PRIDEiP0A8N7

    Interactioni

    Subunit structurei

    Homodimer.UniRule annotation2 Publications

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    aceEP0AFG82EBI-562598,EBI-542683

    Protein-protein interaction databases

    BioGridi4260877, 6 interactors
    DIPiDIP-10535N
    IntActiP0A8N7, 3 interactors
    STRINGi316385.ECDH10B_4350

    Structurei

    Secondary structure

    1325
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi13 – 32Combined sources20
    Beta strandi42 – 46Combined sources5
    Beta strandi57 – 60Combined sources4
    Helixi63 – 65Combined sources3
    Beta strandi69 – 73Combined sources5
    Helixi78 – 86Combined sources9
    Beta strandi91 – 99Combined sources9
    Beta strandi110 – 120Combined sources11
    Helixi124 – 139Combined sources16
    Beta strandi145 – 148Combined sources4
    Helixi149 – 156Combined sources8
    Turni161 – 163Combined sources3
    Helixi166 – 170Combined sources5
    Helixi172 – 175Combined sources4
    Helixi179 – 182Combined sources4
    Helixi190 – 199Combined sources10
    Helixi201 – 203Combined sources3
    Beta strandi204 – 208Combined sources5
    Beta strandi210 – 213Combined sources4
    Helixi217 – 219Combined sources3
    Beta strandi232 – 240Combined sources9
    Beta strandi243 – 251Combined sources9
    Helixi255 – 271Combined sources17
    Helixi281 – 289Combined sources9
    Beta strandi293 – 300Combined sources8
    Helixi301 – 309Combined sources9
    Helixi314 – 317Combined sources4
    Beta strandi318 – 320Combined sources3
    Turni322 – 324Combined sources3

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    3A5YX-ray1.90A/B/C/D1-325[»]
    3A5ZX-ray2.50A/C/E/G1-325[»]
    ProteinModelPortaliP0A8N7
    SMRiP0A8N7
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni76 – 78Substrate binding3

    Sequence similaritiesi

    Belongs to the class-II aminoacyl-tRNA synthetase family. EpmA subfamily.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4105CAP Bacteria
    COG2269 LUCA
    HOGENOMiHOG000236579
    InParanoidiP0A8N7
    KOiK04568
    OMAiEWYRPGF
    PhylomeDBiP0A8N7

    Family and domain databases

    HAMAPiMF_00174 EF_P_modif_A, 1 hit
    InterProiView protein in InterPro
    IPR004364 aa-tRNA-synt_II
    IPR006195 aa-tRNA-synth_II
    IPR004525 EpmA
    IPR018149 Lys-tRNA-synth_II_C
    PfamiView protein in Pfam
    PF00152 tRNA-synt_2, 1 hit
    PRINTSiPR00982 TRNASYNTHLYS
    TIGRFAMsiTIGR00462 genX, 1 hit
    PROSITEiView protein in PROSITE
    PS50862 AA_TRNA_LIGASE_II, 1 hit

    Sequencei

    Sequence statusi: Complete.

    P0A8N7-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSETASWQPS ASIPNLLKRA AIMAEIRRFF ADRGVLEVET PCMSQATVTD
    60 70 80 90 100
    IHLVPFETRF VGPGHSQGMN LWLMTSPEYH MKRLLVAGCG PVFQLCRSFR
    110 120 130 140 150
    NEEMGRYHNP EFTMLEWYRP HYDMYRLMNE VDDLLQQVLD CPAAESLSYQ
    160 170 180 190 200
    QAFLRYLEID PLSADKTQLR EVAAKLDLSN VADTEEDRDT LLQLLFTFGV
    210 220 230 240 250
    EPNIGKEKPT FVYHFPASQA SLAQISTEDH RVAERFEVYY KGIELANGFH
    260 270 280 290 300
    ELTDAREQQQ RFEQDNRKRA ARGLPQHPID QNLIEALKVG MPDCSGVALG
    310 320
    VDRLVMLALG AETLAEVIAF SVDRA
    Length:325
    Mass (Da):36,976
    Last modified:June 7, 2005 - v1
    Checksum:iF72B535CCA23E4CC
    GO

    Sequence cautioni

    The sequence AAA97054 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti78E → Q in AAA23436 (PubMed:7037404).Curated1
    Sequence conflicti144A → E in AAA23436 (PubMed:7037404).Curated1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X59988 Genomic DNA Translation: CAA42604.1
    U14003 Genomic DNA Translation: AAA97054.1 Different initiation.
    U00096 Genomic DNA Translation: AAC77115.2
    AP009048 Genomic DNA Translation: BAE78159.1
    J01611 Genomic DNA Translation: AAA23436.2
    PIRiS56383
    RefSeqiNP_418579.2, NC_000913.3
    WP_000004771.1, NZ_LN832404.1

    Genome annotation databases

    EnsemblBacteriaiAAC77115; AAC77115; b4155
    BAE78159; BAE78159; BAE78159
    GeneIDi948672
    KEGGiecj:JW4116
    eco:b4155
    PATRICifig|1411691.4.peg.2543

    Similar proteinsi

    Entry informationi

    Entry nameiEPMA_ECOLI
    AccessioniPrimary (citable) accession number: P0A8N7
    Secondary accession number(s): P03812
    , P78141, Q2M6E7, Q8XDP9
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: June 7, 2005
    Last modified: March 28, 2018
    This is version 109 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. SIMILARITY comments
      Index of protein domains and families
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