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Protein

Elongation factor P

Gene

efp

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in peptide bond synthesis. Alleviates ribosome stalling that occurs when 3 or more consecutive Pro residues or the sequence PPG is present in a protein, possibly by augmenting the peptidyl transferase activity of the ribosome. Beta-lysylation at Lys-34 is required for alleviation. The Pro codons and their context do not affect activity; only consecutive Pro residues (not another amino acid) are affected by EF-P. Has stimulatory effects on peptide bond formation between ribosome-bound initiator tRNA(fMet) and puromycin, and N-acetyl-Phe tRNA(Phe)-primed poly(U)-directed poly(Phe) synthesis.2 Publications

Pathwayi: polypeptide chain elongation

This protein is involved in the pathway polypeptide chain elongation, which is part of Protein biosynthesis.
View all proteins of this organism that are known to be involved in the pathway polypeptide chain elongation and in Protein biosynthesis.

GO - Molecular functioni

  • ribosome binding Source: EcoCyc
  • translation elongation factor activity Source: EcoCyc

GO - Biological processi

  • translational elongation Source: EcoCyc
Complete GO annotation...

Keywords - Molecular functioni

Elongation factor

Keywords - Biological processi

Protein biosynthesis

Enzyme and pathway databases

BioCyciEcoCyc:EG12099-MONOMER.
ECOL316407:JW4107-MONOMER.
MetaCyc:EG12099-MONOMER.
UniPathwayiUPA00345.

Names & Taxonomyi

Protein namesi
Recommended name:
Elongation factor P
Short name:
EF-P
Gene namesi
Name:efp
Ordered Locus Names:b4147, JW4107
OrganismiEscherichia coli (strain K12)
Taxonomic identifieri83333 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
Proteomesi
  • UP000000318 Componenti: Chromosome
  • UP000000625 Componenti: Chromosome

Organism-specific databases

EcoGeneiEG12099. efp.

Subcellular locationi

GO - Cellular componenti

  • cytoplasm Source: EcoCyc
  • cytosol Source: EcoCyc
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

Pathology & Biotechi

Disruption phenotypei

Disruption of this gene leads to lethality (PubMed:9405429) or to a very slow growth phenotype (PubMed:20729861). Required for the expression of poly-Pro-containing proteins.3 Publications

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi31 – 311K → A: No lysylation. 1 Publication
Mutagenesisi33 – 331G → K: No lysylation. Loss of in vivo EF-P function for cell growth. 1 Publication
Mutagenesisi34 – 341K → A: No lysylation and loss of EF-P activity. No facilitation of translation of poly-Pro stretches. 3 Publications

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemoved2 Publications
Chaini2 – 188187Elongation factor PPRO_0000094245Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei34 – 341N6-(3,6-diaminohexanoyl)-5-hydroxylysine3 Publications

Post-translational modificationi

Is beta-lysylated on the epsilon-amino group of Lys-34 by the combined action of EpmA and EpmB, and then hydroxylated on the C5 position of the same residue by EpmC. Lysylation is critical for the stimulatory effect of EF-P on peptide-bond formation. The lysylation moiety would extend toward the peptidyltransferase center and stabilize the terminal 3-CCA end of the tRNA. The hydroxylation of the C5 position on Lys-34 would allow additional potential stabilizing hydrogen-bond interactions with the P-tRNA (PubMed:21841797 PubMed:22128152 PubMed:22706199 and PubMed:20729861).3 Publications

Keywords - PTMi

Hydroxylation

Proteomic databases

EPDiP0A6N4.
PaxDbiP0A6N4.
PRIDEiP0A6N4.

Interactioni

Subunit structurei

Binds 30S, 50S and 70S ribosomes, possibly near the A site, note that T.thermophilus structures show binding between the P and E sites (PDB 3HUW and 3HUY). Proportionally less EF-P binds to larger polysomes, suggesting it has a role early in translation. It is present in 1 copy per 10 ribosomes.1 Publication

Protein-protein interaction databases

BioGridi4260776. 698 interactions.
DIPiDIP-31834N.
IntActiP0A6N4. 1 interaction.
STRINGi511145.b4147.

Structurei

Secondary structure

1
188
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi4 – 63Combined sources
Beta strandi14 – 174Combined sources
Beta strandi20 – 3011Combined sources
Beta strandi38 – 458Combined sources
Helixi46 – 483Combined sources
Beta strandi51 – 577Combined sources
Beta strandi61 – 644Combined sources
Beta strandi67 – 704Combined sources
Beta strandi73 – 775Combined sources
Beta strandi82 – 854Combined sources
Turni87 – 893Combined sources
Beta strandi92 – 954Combined sources
Helixi97 – 1004Combined sources
Turni102 – 1065Combined sources
Beta strandi109 – 1124Combined sources
Beta strandi114 – 1185Combined sources
Beta strandi121 – 1266Combined sources
Beta strandi152 – 1565Combined sources
Beta strandi161 – 1644Combined sources
Beta strandi173 – 1775Combined sources
Turni178 – 1814Combined sources
Beta strandi182 – 1865Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3A5ZX-ray2.50B/D/F/H1-188[»]
ProteinModelPortaliP0A6N4.
SMRiP0A6N4. Positions 3-187.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the elongation factor P family.Curated

Phylogenomic databases

eggNOGiENOG4105DRH. Bacteria.
COG0231. LUCA.
HOGENOMiHOG000010047.
InParanoidiP0A6N4.
KOiK02356.
OMAiDYVFMDM.
OrthoDBiEOG6JQH6Q.
PhylomeDBiP0A6N4.

Family and domain databases

Gene3Di2.30.30.30. 1 hit.
2.40.50.140. 2 hits.
HAMAPiMF_00141. EF_P.
InterProiIPR015365. Elong-fact-P_C.
IPR012340. NA-bd_OB-fold.
IPR014722. Rib_L2_dom2.
IPR020599. Transl_elong_fac_P/YeiP.
IPR013185. Transl_elong_KOW-like.
IPR001059. Transl_elong_P/YeiP_cen.
IPR013852. Transl_elong_P/YeiP_CS.
IPR011768. Transl_elongation_fac_P.
IPR008991. Translation_prot_SH3-like.
[Graphical view]
PfamiPF01132. EFP. 1 hit.
PF08207. EFP_N. 1 hit.
PF09285. Elong-fact-P_C. 1 hit.
[Graphical view]
PIRSFiPIRSF005901. EF-P. 1 hit.
SMARTiSM01185. EFP. 1 hit.
SM00841. Elong-fact-P_C. 1 hit.
[Graphical view]
SUPFAMiSSF50104. SSF50104. 1 hit.
SSF50249. SSF50249. 2 hits.
TIGRFAMsiTIGR00038. efp. 1 hit.
PROSITEiPS01275. EFP. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P0A6N4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MATYYSNDFR AGLKIMLDGE PYAVEASEFV KPGKGQAFAR VKLRRLLTGT
60 70 80 90 100
RVEKTFKSTD SAEGADVVDM NLTYLYNDGE FWHFMNNETF EQLSADAKAI
110 120 130 140 150
GDNAKWLLDQ AECIVTLWNG QPISVTPPNF VELEIVDTDP GLKGDTAGTG
160 170 180
GKPATLSTGA VVKVPLFVQI GEVIKVDTRS GEYVSRVK
Length:188
Mass (Da):20,591
Last modified:January 23, 2007 - v2
Checksum:iE36E136D4399460F
GO

Mass spectrometryi

Molecular mass is 20591.6 Da from positions 2 - 188. Determined by ESI. With N6-(3,6-diaminohexanoyl)-5-hydroxy-Lys-34.1 Publication

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X61676 Genomic DNA. Translation: CAA43851.1.
U14003 Genomic DNA. Translation: AAA97046.1.
U00096 Genomic DNA. Translation: AAC77107.1.
AP009048 Genomic DNA. Translation: BAE78149.1.
PIRiS34443.
RefSeqiNP_418571.1. NC_000913.3.
WP_000257278.1. NZ_LN832404.1.

Genome annotation databases

EnsemblBacteriaiAAC77107; AAC77107; b4147.
BAE78149; BAE78149; BAE78149.
GeneIDi948661.
KEGGiecj:JW4107.
eco:b4147.
PATRICi32123863. VBIEscCol129921_4279.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X61676 Genomic DNA. Translation: CAA43851.1.
U14003 Genomic DNA. Translation: AAA97046.1.
U00096 Genomic DNA. Translation: AAC77107.1.
AP009048 Genomic DNA. Translation: BAE78149.1.
PIRiS34443.
RefSeqiNP_418571.1. NC_000913.3.
WP_000257278.1. NZ_LN832404.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3A5ZX-ray2.50B/D/F/H1-188[»]
ProteinModelPortaliP0A6N4.
SMRiP0A6N4. Positions 3-187.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi4260776. 698 interactions.
DIPiDIP-31834N.
IntActiP0A6N4. 1 interaction.
STRINGi511145.b4147.

Proteomic databases

EPDiP0A6N4.
PaxDbiP0A6N4.
PRIDEiP0A6N4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAC77107; AAC77107; b4147.
BAE78149; BAE78149; BAE78149.
GeneIDi948661.
KEGGiecj:JW4107.
eco:b4147.
PATRICi32123863. VBIEscCol129921_4279.

Organism-specific databases

EchoBASEiEB2023.
EcoGeneiEG12099. efp.

Phylogenomic databases

eggNOGiENOG4105DRH. Bacteria.
COG0231. LUCA.
HOGENOMiHOG000010047.
InParanoidiP0A6N4.
KOiK02356.
OMAiDYVFMDM.
OrthoDBiEOG6JQH6Q.
PhylomeDBiP0A6N4.

Enzyme and pathway databases

UniPathwayiUPA00345.
BioCyciEcoCyc:EG12099-MONOMER.
ECOL316407:JW4107-MONOMER.
MetaCyc:EG12099-MONOMER.

Miscellaneous databases

PROiP0A6N4.

Family and domain databases

Gene3Di2.30.30.30. 1 hit.
2.40.50.140. 2 hits.
HAMAPiMF_00141. EF_P.
InterProiIPR015365. Elong-fact-P_C.
IPR012340. NA-bd_OB-fold.
IPR014722. Rib_L2_dom2.
IPR020599. Transl_elong_fac_P/YeiP.
IPR013185. Transl_elong_KOW-like.
IPR001059. Transl_elong_P/YeiP_cen.
IPR013852. Transl_elong_P/YeiP_CS.
IPR011768. Transl_elongation_fac_P.
IPR008991. Translation_prot_SH3-like.
[Graphical view]
PfamiPF01132. EFP. 1 hit.
PF08207. EFP_N. 1 hit.
PF09285. Elong-fact-P_C. 1 hit.
[Graphical view]
PIRSFiPIRSF005901. EF-P. 1 hit.
SMARTiSM01185. EFP. 1 hit.
SM00841. Elong-fact-P_C. 1 hit.
[Graphical view]
SUPFAMiSSF50104. SSF50104. 1 hit.
SSF50249. SSF50249. 2 hits.
TIGRFAMsiTIGR00038. efp. 1 hit.
PROSITEiPS01275. EFP. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Cloning, sequencing and overexpression of the gene for prokaryotic factor EF-P involved in peptide bond synthesis."
    Aoki H., Adams S.-L., Chung D.-G., Yaguchi M., Chuang S.-E., Ganoza M.C.
    Nucleic Acids Res. 19:6215-6220(1991) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 2-33; 71-80 AND 86-117.
  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. 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. "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12."
    Link A.J., Robison K., Church G.M.
    Electrophoresis 18:1259-1313(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-13.
    Strain: K12 / EMG2.
  6. "Molecular characterization of the prokaryotic efp gene product involved in a peptidyltransferase reaction."
    Aoki H., Adams S.-L., Turner M.A., Ganoza M.C.
    Biochimie 79:7-11(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: CHARACTERIZATION.
  7. "The gene encoding the elongation factor P protein is essential for viability and is required for protein synthesis."
    Aoki H., Dekany K., Adams S.L., Ganoza M.C.
    J. Biol. Chem. 272:32254-32259(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: DISRUPTION PHENOTYPE.
  8. "Identification and quantitation of elongation factor EF-P in Escherichia coli cell-free extracts."
    An G., Glick B.R., Friesen J.D., Ganoza M.C.
    Can. J. Biochem. 58:1312-1314(1980) [PubMed] [Europe PMC] [Abstract]
    Cited for: COPY NUMBER.
  9. "Interactions of elongation factor EF-P with the Escherichia coli ribosome."
    Aoki H., Xu J., Emili A., Chosay J.G., Golshani A., Ganoza M.C.
    FEBS J. 275:671-681(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: PTM, RIBOSOME-BINDING.
  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: BETA-LYSYLATION AT LYS-34 BY EPMA.
    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: BETA-LYSYLATION AT LYS-34 BY EPMA AND EPMB, MUTAGENESIS OF LYS-34.
    Strain: K12 / MG1655 / ATCC 47076 and MRE-600.
  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: BETA-LYSYLATION AT LYS-34 BY EPMC, MASS SPECTROMETRY.
    Strain: K12 / AT713, K12 / BW25113, K12 / MC4100 / ATCC 35695 / DSM 6574 and MRE-600.
  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: FUNCTION IN POLY-PRO TRANSLATION, DISRUPTION PHENOTYPE, MUTAGENESIS OF LYS-34.
    Strain: K12 / BW25113 and K12 / MG1655 / ATCC 47076.
  14. "EF-P is essential for rapid synthesis of proteins containing consecutive proline residues."
    Doerfel L.K., Wohlgemuth I., Kothe C., Peske F., Urlaub H., Rodnina M.V.
    Science 339:85-88(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN TRANSLATION, PTM.
    Strain: B / BL21-DE3 and MRE-600.
  15. "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 (2.50 ANGSTROMS) IN COMPLEX WITH LYSYL-ADENYLATE ANALOG AND EMPA, DISRUPTION PHENOTYPE, MUTAGENESIS OF LYS-31; GLY-33 AND LYS-34.
    Strain: K12 / BW25113 and K12 / MC4100 / ATCC 35695 / DSM 6574.

Entry informationi

Entry nameiEFP_ECOLI
AccessioniPrimary (citable) accession number: P0A6N4
Secondary accession number(s): P33398, Q2M6F7
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 10, 2005
Last sequence update: January 23, 2007
Last modified: May 11, 2016
This is version 97 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Caution

The modification on Lys-34 was initially thought to be a spermidine residue.1 Publication

Keywords - Technical termi

3D-structure, Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Escherichia coli
    Escherichia coli (strain K12): entries and cross-references to EcoGene
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. 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.