Elongation factor P--(R)-beta-lysine ligase - Escherichia coli (strain K12)

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P0A8N7 (EPMA_ECOLI) Reviewed, UniProtKB/Swiss-Prot

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

Clusters with 100%, 90%, 50% identity |

Documents (3) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended 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

Organism

Escherichia coli (strain K12) [Reference proteome] [HAMAP]

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

Bacteria › Proteobacteria › Gammaproteobacteria › Enterobacteriales › Enterobacteriaceae › Escherichia ›

Protein attributes

Sequence length	325 AA.
Sequence status	Complete.
Protein existence	Evidence 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. K_M=213 µM for (R)-beta-lysine Ref.10 K_M=8600 µM for L-alpha-lysine K_M=6950 µM for (S)-beta-lysine K_M=206 µM for ATP
Sequence caution	The sequence AAA97054.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.

Ontologies

Keywords
Ligand	ATP-binding Nucleotide-binding
Molecular function	Ligase
Technical term	3D-structure Complete proteome Reference proteome
Gene Ontology (GO)
Biological_process	lysyl-tRNA aminoacylation Inferred from electronic annotation. Source: InterPro protein-N6-(L-lysyl)-L-lysine modification to protein-N6-(beta-lysyl)-L-lysine Inferred from direct assay Ref.11. Source: EcoCyc protein-lysine lysylation Inferred from direct assay Ref.14. Source: EcoCyc
Cellular_component	cytoplasm Inferred from electronic annotation. Source: InterPro
Molecular_function	ATP binding Inferred from electronic annotation. Source: HAMAP acid-ammonia (or amide) ligase activity Inferred from electronic annotation. Source: HAMAP lysine-tRNA ligase activity Inferred from electronic annotation. Source: InterPro protein-lysine lysyltransferase activity Inferred from direct assay Ref.14. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Chain

1 – 325

325

Elongation factor P--(R)-beta-lysine ligase HAMAP-Rule MF_00174

PRO_0000152719

Regions

Nucleotide binding

100 – 102

ATP HAMAP-Rule MF_00174

Nucleotide binding

244 – 245

ATP HAMAP-Rule MF_00174

Region

76 – 78

Substrate binding HAMAP-Rule MF_00174

Sites

Binding site

109

ATP; via amide nitrogen and carbonyl oxygen

Binding site

118

Substrate

Binding site

251

Substrate

Binding site

300

ATP; via amide nitrogen

Experimental info

Mutagenesis

D → A: No effect on lysylation activity. Ref.14

Mutagenesis

S → A: Loss of catalytic activity. Ref.10

Mutagenesis

100

R → A: Loss of lysylation activity. Ref.14

Mutagenesis

102

E → A: No effect on lysylation activity. Ref.14

Mutagenesis

103

E → A: Loss of lysylation activity. Ref.14

Mutagenesis

108

H → A: Severe reduction in lysylation activity. Ref.14

Mutagenesis

185

E → A: Slight reduction in lysylation activity. Ref.14

Mutagenesis

193

Q → A: Slight reduction in lysylation activity. Ref.14

Mutagenesis

244

E → A: Loss of lysylation activity. Ref.14

Mutagenesis

247

N → A: Loss of lysylation activity. Ref.14

Mutagenesis

298

A → 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

Mutagenesis

303

R → A: Loss of lysylation activity. Ref.14

Sequence conflict

E → Q in AAA23436. Ref.5

Sequence conflict

144

A → E in AAA23436. Ref.5

Sequences

Sequence

Length

Mass (Da)

Tools

P0A8N7 [UniParc].

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

325

36,976

        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' referencesShow '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.

PIR

S56383.

RefSeq

NP_418579.2. NC_000913.2.
YP_492300.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3A5Y	X-ray	1.90	A/B/C/D	1-325	[»]
3A5Z	X-ray	2.50	A/C/E/G	1-325	[»]

ProteinModelPortal

P0A8N7.

SMR

P0A8N7. Positions 2-325.

ModBase

Search...

Protein-protein interaction databases

IntAct

P0A8N7. 3 interactions.

STRING

511145.b4155.

Proteomic databases

PaxDb

P0A8N7.

PRIDE

P0A8N7.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC77115; AAC77115; b4155.
BAE78159; BAE78159; BAE78159.

GeneID

12931883.
948672.

KEGG

ecj:Y75_p4044.
eco:b4155.

PATRIC

32123883. VBIEscCol129921_4289.

Organism-specific databases

EchoBASE

EB1196.

EcoGene

EG11211. epmA.

Phylogenomic databases

eggNOG

COG2269.

HOGENOM

HOG000236579.

K04568.

OMA

MPEASGI.

ProtClustDB

PRK09350.

Enzyme and pathway databases

BioCyc

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

Gene expression databases

Genevestigator

P0A8N7.

Family and domain databases

HAMAP

MF_00174. EF-P_modif_A.

InterPro

IPR004364. 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]

PANTHER

PTHR22594. PTHR22594. 1 hit.
PTHR22594:SF7. PTHR22594:SF7. 1 hit.

Pfam

PF00152. tRNA-synt_2. 1 hit.
[Graphical view]

PRINTS

PR00982. TRNASYNTHLYS.

TIGRFAMs

TIGR00462. genX. 1 hit.

PROSITE

PS50862. AA_TRNA_LIGASE_II. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

EPMA_ECOLI

Accession

Primary (citable) accession number: P0A8N7
Secondary accession number(s): P03812

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 status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic 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

Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Regions

Sites

Experimental info

Sequences

References

Cross-references

Sequence databases

3D structure databases

Protein-protein interaction databases

Proteomic databases

Protocols and materials databases

Genome annotation databases

Organism-specific databases

Phylogenomic databases

Enzyme and pathway databases

Gene expression databases

Family and domain databases

Entry information

Relevant documents