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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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei109 – 1091ATP; via amide nitrogen and carbonyl oxygen
    Binding sitei118 – 1181Substrate
    Binding sitei251 – 2511Substrate
    Binding sitei300 – 3001ATP; via amide nitrogen

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi100 – 1023ATP
    Nucleotide bindingi244 – 2452ATP

    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    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)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi50 – 501D → A: No effect on lysylation activity. 1 Publication
    Mutagenesisi76 – 761S → A: Loss of catalytic activity. 1 Publication
    Mutagenesisi100 – 1001R → A: Loss of lysylation activity. 1 Publication
    Mutagenesisi102 – 1021E → A: No effect on lysylation activity. 1 Publication
    Mutagenesisi103 – 1031E → A: Loss of lysylation activity. 1 Publication
    Mutagenesisi108 – 1081H → A: Severe reduction in lysylation activity. 1 Publication
    Mutagenesisi185 – 1851E → A: Slight reduction in lysylation activity. 1 Publication
    Mutagenesisi193 – 1931Q → A: Slight reduction in lysylation activity. 1 Publication
    Mutagenesisi244 – 2441E → A: Loss of lysylation activity. 1 Publication
    Mutagenesisi247 – 2471N → A: Loss of lysylation activity. 1 Publication
    Mutagenesisi298 – 2981A → 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 Publication
    Mutagenesisi303 – 3031R → A: Loss of lysylation activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 325325Elongation factor P--(R)-beta-lysine ligasePRO_0000152719Add
    BLAST

    Proteomic databases

    PaxDbiP0A8N7.
    PRIDEiP0A8N7.

    Interactioni

    Subunit structurei

    Homodimer.UniRule annotation2 Publications

    Protein-protein interaction databases

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

    Structurei

    Secondary structure

    1
    325
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi13 – 3220Combined sources
    Beta strandi42 – 465Combined sources
    Beta strandi57 – 604Combined sources
    Helixi63 – 653Combined sources
    Beta strandi69 – 735Combined sources
    Helixi78 – 869Combined sources
    Beta strandi91 – 999Combined sources
    Beta strandi110 – 12011Combined sources
    Helixi124 – 13916Combined sources
    Beta strandi145 – 1484Combined sources
    Helixi149 – 1568Combined sources
    Turni161 – 1633Combined sources
    Helixi166 – 1705Combined sources
    Helixi172 – 1754Combined sources
    Helixi179 – 1824Combined sources
    Helixi190 – 19910Combined sources
    Helixi201 – 2033Combined sources
    Beta strandi204 – 2085Combined sources
    Beta strandi210 – 2134Combined sources
    Helixi217 – 2193Combined sources
    Beta strandi232 – 2409Combined sources
    Beta strandi243 – 2519Combined sources
    Helixi255 – 27117Combined sources
    Helixi281 – 2899Combined sources
    Beta strandi293 – 3008Combined sources
    Helixi301 – 3099Combined sources
    Helixi314 – 3174Combined sources
    Beta strandi318 – 3203Combined sources
    Turni322 – 3243Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3A5YX-ray1.90A/B/C/D1-325[»]
    3A5ZX-ray2.50A/C/E/G1-325[»]
    ProteinModelPortaliP0A8N7.
    SMRiP0A8N7. Positions 2-325.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni76 – 783Substrate binding

    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)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti78 – 781E → Q in AAA23436 (PubMed:7037404).Curated
    Sequence conflicti144 – 1441A → E in AAA23436 (PubMed:7037404).Curated

    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
    EntryMethodResolution (Å)ChainPositionsPDBsum
    3A5YX-ray1.90A/B/C/D1-325[»]
    3A5ZX-ray2.50A/C/E/G1-325[»]
    ProteinModelPortaliP0A8N7.
    SMRiP0A8N7. Positions 2-325.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4260877. 6 interactions.
    DIPiDIP-10535N.
    IntActiP0A8N7. 3 interactions.
    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: September 7, 2016
    This is version 100 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.