Elongation factor P - Escherichia coli (strain K12)

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P0A6N4 (EFP_ECOLI) Reviewed, UniProtKB/Swiss-Prot

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

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

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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
Short name=EF-P

Gene names

Name:	efp
Ordered Locus Names:	b4147, JW4107

Organism

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

Taxonomic identifier

83333 [NCBI]

Taxonomic lineage

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

Protein attributes

Sequence length	188 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level

General annotation (Comments)

Function	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. Ref.13 Ref.14
Pathway	Protein biosynthesis; polypeptide chain elongation. HAMAP-Rule MF_00141
Subunit structure	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.
Subcellular location	Cytoplasm HAMAP-Rule MF_00141.
Post-translational modification	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 (Ref.10 Ref.11 Ref.12 and Ref.15). HAMAP-Rule MF_00141
Disruption phenotype	Disruption of this gene leads to lethality (Ref.7) or to a very slow growth phenotype (Ref.15). Required for the expression of poly-Pro-containing proteins. Ref.7 Ref.13 Ref.15
Sequence similarities	Belongs to the elongation factor P family.
Caution	The modification on Lys-34 was initially thought to be a spermidine residue (Ref.9).
Mass spectrometry	Molecular mass is 20591.6 Da from positions 2 - 188. Determined by ESI. With N6-(3,6-diaminohexanoyl)-5-hydroxy-Lys-34. Ref.12

Ontologies

Keywords
Biological process	Protein biosynthesis
Cellular component	Cytoplasm
Molecular function	Elongation factor
PTM	Hydroxylation
Technical term	3D-structure Complete proteome Direct protein sequencing Reference proteome
Gene Ontology (GO)
Biological_process	peptide biosynthetic process Inferred from electronic annotation. Source: InterPro
Cellular_component	cytoplasm Inferred from direct assay PubMed 1105576. Source: EcoCyc
Molecular_function	ribosome binding Inferred from direct assay Ref.9. Source: EcoCyc translation elongation factor activity Inferred from direct assay PubMed 1105576. Source: EcoCyc
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

Removed Ref.1 Ref.5

Chain

2 – 188

187

Elongation factor P HAMAP-Rule MF_00141

PRO_0000094245

Amino acid modifications

Modified residue

N6-(3,6-diaminohexanoyl)-5-hydroxylysine Ref.12

Experimental info

Mutagenesis

K → A: No lysylation. Ref.15

Mutagenesis

G → K: No lysylation. Loss of in vivo EF-P function for cell growth. Ref.15

Mutagenesis

K → A: No lysylation and loss of EF-P activity. No facilitation of translation of poly-Pro stretches. Ref.11 Ref.13 Ref.15

Sequences

Sequence

Length

Mass (Da)

Tools

P0A6N4 [UniParc].

Last modified January 23, 2007. Version 2.
Checksum: E36E136D4399460F
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FASTA

188

20,591

        10         20         30         40         50         60 
MATYYSNDFR AGLKIMLDGE PYAVEASEFV KPGKGQAFAR VKLRRLLTGT RVEKTFKSTD 

        70         80         90        100        110        120 
SAEGADVVDM NLTYLYNDGE FWHFMNNETF EQLSADAKAI GDNAKWLLDQ AECIVTLWNG 

       130        140        150        160        170        180 
QPISVTPPNF VELEIVDTDP GLKGDTAGTG GKPATLSTGA VVKVPLFVQI GEVIKVDTRS 


GEYVSRVK

« Hide

References

	« Hide 'large scale' referencesShow 'large scale' references »
[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]	"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]	"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: PUTATIVE 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: HYDROXYLATION 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.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

X61676 Genomic DNA. Translation: CAA43851.1.
U14003 Genomic DNA. Translation: AAA97046.1.
U00096 Genomic DNA. Translation: AAC77107.1.
AP009048 Genomic DNA. Translation: BAE78149.1.

PIR

S34443.

RefSeq

NP_418571.1. NC_000913.2.
YP_492290.1. NC_007779.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
3A5Z	X-ray	2.50	B/D/F/H	1-188	[»]

ProteinModelPortal

P0A6N4.

SMR

P0A6N4. Positions 3-187.

ModBase

Search...

Protein-protein interaction databases

DIP

DIP-31834N.

IntAct

P0A6N4. 1 interaction.

STRING

511145.b4147.

Proteomic databases

PaxDb

P0A6N4.

PRIDE

P0A6N4.

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Genome annotation databases

EnsemblBacteria

AAC77107; AAC77107; b4147.
BAE78149; BAE78149; BAE78149.

GeneID

12931782.
948661.

KEGG

ecj:Y75_p4034.
eco:b4147.

PATRIC

32123863. VBIEscCol129921_4279.

Organism-specific databases

EchoBASE

EB2023.

EcoGene

EG12099. efp.

Phylogenomic databases

eggNOG

COG0231.

HOGENOM

HOG000010047.

K02356.

OMA

DSAKWLQ.

ProtClustDB

PRK00529.

Enzyme and pathway databases

BioCyc

EcoCyc:EG12099-MONOMER.
ECOL316407:JW4107-MONOMER.
MetaCyc:EG12099-MONOMER.

UniPathway

UPA00345.

Gene expression databases

Genevestigator

P0A6N4.

Family and domain databases

Gene3D

2.30.30.30. 1 hit.
2.40.50.140. 2 hits.

HAMAP

MF_00141. EF-P.

InterPro

IPR015365. 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]

Pfam

PF01132. EFP. 1 hit.
PF08207. EFP_N. 1 hit.
PF09285. Elong-fact-P_C. 1 hit.
[Graphical view]

PIRSF

PIRSF005901. EF-P. 1 hit.

SMART

SM00841. Elong-fact-P_C. 1 hit.
[Graphical view]

SUPFAM

SSF50249. Nucleic_acid_OB. 2 hits.
SSF50104. Transl_SH3_like. 1 hit.

TIGRFAMs

TIGR00038. efp. 1 hit.

PROSITE

PS01275. EFP. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

EFP_ECOLI

Accession

Primary (citable) accession number: P0A6N4
Secondary accession number(s): P33398, Q2M6F7

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 10, 2005
Last sequence update:	January 23, 2007
Last modified:	May 1, 2013
This is version 76 of the entry and version 2 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

PATHWAY comments

Index of metabolic and biosynthesis pathways

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

Preferred order of sections

Names and origin

Protein attributes

General annotation (Comments)

Ontologies

Sequence annotation (Features)

Molecule processing

Amino acid modifications

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