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P0A8N7 (EPMA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

Last modified May 1, 2013. Version 76. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Elongation factor P--(R)-beta-lysine ligase

Short name=EF-P--(R)-beta-lysine ligase
EC=6.3.1.-
Alternative name(s):
EF-P post-translational modification enzyme A
EF-P-lysine lysyltransferase
GX
Gene names
Name:epmA
Synonyms:genX, poxA, yjeA
Ordered Locus Names:b4155, JW4116
OrganismEscherichia coli (strain K12) [Reference proteome] [HAMAP]
Taxonomic identifier83333 [NCBI]
Taxonomic lineageBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia

Protein attributes

Sequence length325 AA.
Sequence statusComplete.
Protein existenceEvidence at protein level

General annotation (Comments)

Function

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. Ref.9 Ref.10 Ref.11 Ref.14

Subunit structure

Homodimer. Ref.8 Ref.14

Disruption phenotype

Cells have a reduced pyruvate oxidase activity and a reduced growth rate. Cells lack CadA activity (lysine decarboxylase). Ref.6 Ref.13 Ref.14

Sequence similarities

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

Caution

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

Biophysicochemical properties

Kinetic parameters:

kcat is 36 min(-1) for the amino acid activation reaction with (R)-beta-lysine as substrate.

KM=213 µM for (R)-beta-lysine Ref.10

KM=8600 µM for L-alpha-lysine

KM=6950 µM for (S)-beta-lysine

KM=206 µM for ATP

Sequence caution

The sequence AAA97054.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 325325Elongation factor P--(R)-beta-lysine ligase HAMAP-Rule MF_00174
PRO_0000152719

Regions

Nucleotide binding100 – 1023ATP HAMAP-Rule MF_00174
Nucleotide binding244 – 2452ATP HAMAP-Rule MF_00174
Region76 – 783Substrate binding HAMAP-Rule MF_00174

Sites

Binding site1091ATP; via amide nitrogen and carbonyl oxygen
Binding site1181Substrate
Binding site2511Substrate
Binding site3001ATP; via amide nitrogen

Experimental info

Mutagenesis501D → A: No effect on lysylation activity. Ref.14
Mutagenesis761S → A: Loss of catalytic activity. Ref.10
Mutagenesis1001R → A: Loss of lysylation activity. Ref.14
Mutagenesis1021E → A: No effect on lysylation activity. Ref.14
Mutagenesis1031E → A: Loss of lysylation activity. Ref.14
Mutagenesis1081H → A: Severe reduction in lysylation activity. Ref.14
Mutagenesis1851E → A: Slight reduction in lysylation activity. Ref.14
Mutagenesis1931Q → A: Slight reduction in lysylation activity. Ref.14
Mutagenesis2441E → A: Loss of lysylation activity. Ref.14
Mutagenesis2471N → A: Loss of lysylation activity. Ref.14
Mutagenesis2981A → G: 96% increase in the affinity for L-alpha-lysine. 4-fold decrease in the catalytic efficiency of the (R)-beta-lysine activation reaction. Ref.10
Mutagenesis3031R → A: Loss of lysylation activity. Ref.14
Sequence conflict781E → Q in AAA23436. Ref.5
Sequence conflict1441A → E in AAA23436. Ref.5

Sequences

Sequence LengthMass (Da)Tools
P0A8N7 [UniParc].

Last modified June 7, 2005. Version 1.
Checksum: F72B535CCA23E4CC

FASTA32536,976
        10         20         30         40         50         60 
MSETASWQPS ASIPNLLKRA AIMAEIRRFF ADRGVLEVET PCMSQATVTD IHLVPFETRF 

        70         80         90        100        110        120 
VGPGHSQGMN LWLMTSPEYH MKRLLVAGCG PVFQLCRSFR NEEMGRYHNP EFTMLEWYRP 

       130        140        150        160        170        180 
HYDMYRLMNE VDDLLQQVLD CPAAESLSYQ QAFLRYLEID PLSADKTQLR EVAAKLDLSN 

       190        200        210        220        230        240 
VADTEEDRDT LLQLLFTFGV EPNIGKEKPT FVYHFPASQA SLAQISTEDH RVAERFEVYY 

       250        260        270        280        290        300 
KGIELANGFH ELTDAREQQQ RFEQDNRKRA ARGLPQHPID QNLIEALKVG MPDCSGVALG 

       310        320 
VDRLVMLALG AETLAEVIAF SVDRA 

« Hide

References

« Hide 'large scale' references
[1]"Evidence for a new Escherichia coli protein resembling a lysyl-tRNA synthetase."
Kong L., Fromant M., Blanquet S., Plateau P.
Gene 108:163-164(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
[2]"Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes."
Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.
Nucleic Acids Res. 23:2105-2119(1995) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[3]"The complete genome sequence of Escherichia coli K-12."
Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V., Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F., Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B., Shao Y.
Science 277:1453-1474(1997) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / MG1655 / ATCC 47076.
[4]"Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
[5]"Nucleotide sequence coding for the flavoprotein subunit of the fumarate reductase of Escherichia coli."
Cole S.T.
Eur. J. Biochem. 122:479-484(1982) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 1-152.
[6]"Mapping nonselectable genes of Escherichia coli by using transposon Tn10: location of a gene affecting pyruvate oxidase."
Chang Y.-Y., Cronan J.E. Jr.
J. Bacteriol. 151:1279-1289(1982) [PubMed] [Europe PMC] [Abstract]
Cited for: DISRUPTION PHENOTYPE.
Strain: K12.
[7]"Homology of aspartyl- and lysyl-tRNA synthetases."
Gampel A., Tzagoloff A.
Proc. Natl. Acad. Sci. U.S.A. 86:6023-6027(1989) [PubMed] [Europe PMC] [Abstract]
Cited for: SIMILARITY TO CLASS-II AA-TRNA SYNTHETASES.
[8]"Crystallization and preliminary X-ray crystallographic study of GenX, a lysyl-tRNA synthetase paralogue from Escherichia coli, in complex with translation elongation factor P."
Sumida T., Yanagisawa T., Ishii R., Yokoyama S.
Acta Crystallogr. F 66:1115-1118(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: CRYSTALLIZATION, SUBUNIT.
Strain: K12 / MC4100 / ATCC 35695 / DSM 6574.
[9]"Predicting the pathway involved in post-translational modification of Elongation factor P in a subset of bacterial species."
Bailly M., de Crecy-Lagard V.
Biol. Direct 5:3-3(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: POSSIBLE FUNCTION.
[10]"The tRNA synthetase paralog PoxA modifies elongation factor-P with (R)-beta-lysine."
Roy H., Zou S.B., Bullwinkle T.J., Wolfe B.S., Gilreath M.S., Forsyth C.J., Navarre W.W., Ibba M.
Nat. Chem. Biol. 7:667-669(2011) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION, CATALYTIC ACTIVITY, SUBSTRATE SPECIFICITY, KINETIC PARAMETERS, MUTAGENESIS OF SER-76 AND ALA-298.
Strain: K12.
[11]"Post-translational modification by beta-lysylation is required for activity of Escherichia coli elongation factor P (EF-P)."
Park J.H., Johansson H.E., Aoki H., Huang B.X., Kim H.Y., Ganoza M.C., Park M.H.
J. Biol. Chem. 287:2579-2590(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: FUNCTION IN EF-P BETA-LYSYLATION.
Strain: K12 / MG1655 / ATCC 47076.
[12]"Lys34 of translation elongation factor EF-P is hydroxylated by YfcM."
Peil L., Starosta A.L., Virumae K., Atkinson G.C., Tenson T., Remme J., Wilson D.N.
Nat. Chem. Biol. 8:695-697(2012) [PubMed] [Europe PMC] [Abstract]
Cited for: GENE NAME, PATHWAY.
[13]"Translation elongation factor EF-P alleviates ribosome stalling at polyproline stretches."
Ude S., Lassak J., Starosta A.L., Kraxenberger T., Wilson D.N., Jung K.
Science 339:82-85(2013) [PubMed] [Europe PMC] [Abstract]
Cited for: DISRUPTION PHENOTYPE.
Strain: K12 / BW25113 and K12 / MG1655 / ATCC 47076.
[14]"A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P."
Yanagisawa T., Sumida T., Ishii R., Takemoto C., Yokoyama S.
Nat. Struct. Mol. Biol. 17:1136-1143(2010) [PubMed] [Europe PMC] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) IN COMPLEXES WITH LYSYL-ADENYLATE ANALOG AND EF-P, FUNCTION IN EF-P LYSYLATION, SUBUNIT, DISRUPTION PHENOTYPE, MUTAGENESIS OF ASP-50; ARG-100; GLU-102; GLU-103; HIS-108; GLU-185; GLN-193; GLU-244; ASN-247 AND ARG-303.
Strain: K12 / BW25113 and K12 / MC4100 / ATCC 35695 / DSM 6574.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
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.
PIRS56383.
RefSeqNP_418579.2. NC_000913.2.
YP_492300.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
3A5YX-ray1.90A/B/C/D1-325[»]
3A5ZX-ray2.50A/C/E/G1-325[»]
ProteinModelPortalP0A8N7.
SMRP0A8N7. Positions 2-325.
ModBaseSearch...

Protein-protein interaction databases

IntActP0A8N7. 3 interactions.
STRING511145.b4155.

Proteomic databases

PaxDbP0A8N7.
PRIDEP0A8N7.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAAC77115; AAC77115; b4155.
BAE78159; BAE78159; BAE78159.
GeneID12931883.
948672.
KEGGecj:Y75_p4044.
eco:b4155.
PATRIC32123883. VBIEscCol129921_4289.

Organism-specific databases

EchoBASEEB1196.
EcoGeneEG11211. epmA.

Phylogenomic databases

eggNOGCOG2269.
HOGENOMHOG000236579.
KOK04568.
OMAMPEASGI.
ProtClustDBPRK09350.

Enzyme and pathway databases

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

Gene expression databases

GenevestigatorP0A8N7.

Family and domain databases

HAMAPMF_00174. EF-P_modif_A.
InterProIPR004364. aa-tRNA-synt_II.
IPR018150. aa-tRNA-synt_II-like.
IPR006195. aa-tRNA-synth_II.
IPR004525. Lys-tRNA-synth-rel.
IPR018149. Lys-tRNA-synth_II_C.
[Graphical view]
PANTHERPTHR22594. PTHR22594. 1 hit.
PTHR22594:SF7. PTHR22594:SF7. 1 hit.
PfamPF00152. tRNA-synt_2. 1 hit.
[Graphical view]
PRINTSPR00982. TRNASYNTHLYS.
TIGRFAMsTIGR00462. genX. 1 hit.
PROSITEPS50862. AA_TRNA_LIGASE_II. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameEPMA_ECOLI
AccessionPrimary (citable) accession number: P0A8N7
Secondary accession number(s): P03812 expand/collapse secondary AC list , P78141, Q2M6E7, Q8XDP9
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: June 7, 2005
Last modified: May 1, 2013
This is version 76 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Relevant documents

Escherichia coli

Escherichia coli (strain K12): entries and cross-references to EcoGene

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families