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Protein

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

Gene

epmA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

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

    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
    Complete GO annotation...

    Keywords - Molecular functioni

    Ligase

    Keywords - Ligandi

    ATP-binding, Nucleotide-binding

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11211-MONOMER.
    ECOL316407:JW4116-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
    Complete GO annotation...

    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

    Protein-protein interaction databases

    BioGridi4260877. 6 interactors.
    DIPiDIP-10535N.
    IntActiP0A8N7. 3 interactors.
    STRINGi511145.b4155.

    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.
    OMAiEEAGRHH.
    PhylomeDBiP0A8N7.

    Family and domain databases

    HAMAPiMF_00174. EF_P_modif_A. 1 hit.
    InterProiIPR004364. aa-tRNA-synt_II.
    IPR018150. aa-tRNA-synt_II-like.
    IPR006195. aa-tRNA-synth_II.
    IPR004525. EpmA.
    IPR018149. Lys-tRNA-synth_II_C.
    [Graphical view]
    PANTHERiPTHR22594. PTHR22594. 1 hit.
    PTHR22594:SF7. PTHR22594:SF7. 1 hit.
    PfamiPF00152. tRNA-synt_2. 1 hit.
    [Graphical view]
    PRINTSiPR00982. TRNASYNTHLYS.
    TIGRFAMsiTIGR00462. genX. 1 hit.
    PROSITEiPS50862. AA_TRNA_LIGASE_II. 1 hit.
    [Graphical view]

    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.
    PATRICi32123883. VBIEscCol129921_4289.

    Cross-referencesi

    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.

    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...

    Protein-protein interaction databases

    BioGridi4260877. 6 interactors.
    DIPiDIP-10535N.
    IntActiP0A8N7. 3 interactors.
    STRINGi511145.b4155.

    Proteomic databases

    PaxDbiP0A8N7.
    PRIDEiP0A8N7.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC77115; AAC77115; b4155.
    BAE78159; BAE78159; BAE78159.
    GeneIDi948672.
    KEGGiecj:JW4116.
    eco:b4155.
    PATRICi32123883. VBIEscCol129921_4289.

    Organism-specific databases

    EchoBASEiEB1196.
    EcoGeneiEG11211. epmA.

    Phylogenomic databases

    eggNOGiENOG4105CAP. Bacteria.
    COG2269. LUCA.
    HOGENOMiHOG000236579.
    InParanoidiP0A8N7.
    KOiK04568.
    OMAiEEAGRHH.
    PhylomeDBiP0A8N7.

    Enzyme and pathway databases

    BioCyciEcoCyc:EG11211-MONOMER.
    ECOL316407:JW4116-MONOMER.
    MetaCyc:EG11211-MONOMER.

    Miscellaneous databases

    PROiP0A8N7.

    Family and domain databases

    HAMAPiMF_00174. EF_P_modif_A. 1 hit.
    InterProiIPR004364. aa-tRNA-synt_II.
    IPR018150. aa-tRNA-synt_II-like.
    IPR006195. aa-tRNA-synth_II.
    IPR004525. EpmA.
    IPR018149. Lys-tRNA-synth_II_C.
    [Graphical view]
    PANTHERiPTHR22594. PTHR22594. 1 hit.
    PTHR22594:SF7. PTHR22594:SF7. 1 hit.
    PfamiPF00152. tRNA-synt_2. 1 hit.
    [Graphical view]
    PRINTSiPR00982. TRNASYNTHLYS.
    TIGRFAMsiTIGR00462. genX. 1 hit.
    PROSITEiPS50862. AA_TRNA_LIGASE_II. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiEPMA_ECOLI
    AccessioniPrimary (citable) accession number: P0A8N7
    Secondary accession number(s): P03812
    , P78141, Q2M6E7, Q8XDP9
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: July 21, 1986
    Last sequence update: June 7, 2005
    Last modified: November 2, 2016
    This is version 101 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Caution

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

    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

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.