Escherichia coli K-12 substr. MG1655 Polypeptide: protein chain elongation factor EF-P

Gene: efp Accession Numbers: EG12099 (EcoCyc), b4147, ECK4141

Synonyms: EF-P

Regulation Summary Diagram: ?

Regulation summary diagram for efp

Alternative forms of protein chain elongation factor EF-P: protein chain elongation factor EF-P, β-lysyl-Lys34

EF-P is an elongation factor that stimulates the synthesis of peptide bonds [Glick75, Glick79, Ganoza85, Green85, Baxter87, Ganoza00]. EF-P specifically functions to enhance translation of polyproline-containing proteins by alleviating the stalling of ribosomes at polyproline stretches [Ude13, Doerfel13] and for a specific subset of proteins that contain diprolyl motifs (XPP/PPX) [Peil13]. The presence of EF-P only affects the production of a polyproline-containing protein if the translation elongation rate is more affected than translation initiation [Hersch14].

The EF-P binding site on the ribosome overlaps the peptidyltransferase center [Aoki97]; interactions between EF-P and 70S ribosomes have been mapped [Aoki08a]. It was previously thought that EF-P might facilitate proper positioning of fMet-tRNAfMet for initial peptide bond formation [Aoki08a, Blaha09], but [Bullwinkle13] showed no involvement of EF-P in forming the initiation complex.

A screen of Salmonella enterica proteins whose translation is affected by EF-P led to the identification and verification of additional protein sequence motifs present in the affected proteins [Hersch13]. However, EF-P does not affect ribosomal stalling at other short peptide motifs that were identified in a screen in E. coli [Woolstenhulme13]. In certain polyproline-containing proteins, translation does not stall and thus does not depend on EF-P, revealing that certain amino acids upstream of the PPP [Starosta14] and PPX [Elgamal14] motifs influence ribosomal pausing.

EF-P has been reported to be essential for viability by [Aoki97a], but deletion [Balibar13] and transposon insertion [Baba06] mutants were later constructed and shown to have a slow growth phenotype [Baba06, Yanagisawa10, Balibar13]. valyl-tRNA synthetase contains a conserved proline triplet that is critical for activity. ValS requires EF-P for expression, which may explain evolution of the EF-P system [Starosta14a]. E. coli contains approximately one molecule of EF-P per 10 ribosomes [An80]. The EF-P-stimulated synthesis of peptide bonds is one of several targets of the oxazolidinone class of antibiotics [Aoki02].

The Lys34 residue of EF-P is modified; the modification was initially thought to be a spermidine residue [Aoki08a], but was later predicted to be a β-lysine residue [Bailly10]. Further experiments showed that Lys34 is modified with a lysyl residue, which requires both EpmA and EpmB. The β-lysyl-modified form is the active form in vivo [Yanagisawa10, Roy11, Park12, Ude13, Doerfel13]. EpmC was subsequently shown to catalyze the hydroxylation of the γ (C4) or δ (C5) position of Lys34 in EF-P [Peil12]. The 5-hydroxyllysine form of EF-P appears to be present in vivo [Peil12], although hydroxylation does not alter EF-P activity [Doerfel13, Bullwinkle13].

EF-P may form a complex in solution; its molecular weight as measured on a Sephadex column is 50 kD [Glick75]. The activity of EF-P is dependent on Mg2+ ions [Glick75]. EF-P is phosphorylated in bacteriophage T7-infected cells [Robertson94].

A K34A mutant of efp is not lysylated, showing that K34 is the only lysylation site in EF-P. The site was also identified by mass spectrometry [Park12].

Review: [Buskirk13]

Citations: [Sumida10, Mandal14]

Locations: cytosol

Map Position: [4,373,722 -> 4,374,288] (94.27 centisomes, 339°)
Length: 567 bp / 188 aa

Molecular Weight of Polypeptide: 20.591 kD (from nucleotide sequence), 21 kD (experimental) [Glick79a ]

Unification Links: ASAP:ABE-0013583 , CGSC:34470 , DIP:DIP-31834N , EchoBASE:EB2023 , EcoGene:EG12099 , EcoliWiki:b4147 , OU-Microarray:b4147 , PortEco:efp , PR:PRO_000022504 , Pride:P0A6N4 , Protein Model Portal:P0A6N4 , RefSeq:NP_418571 , RegulonDB:EG12099 , SMR:P0A6N4 , String:511145.b4147 , Swiss-Model:P0A6N4 , UniProt:P0A6N4

Relationship Links: InterPro:IN-FAMILY:IPR001059 , InterPro:IN-FAMILY:IPR008991 , InterPro:IN-FAMILY:IPR011768 , InterPro:IN-FAMILY:IPR012340 , InterPro:IN-FAMILY:IPR013185 , InterPro:IN-FAMILY:IPR013852 , InterPro:IN-FAMILY:IPR014722 , InterPro:IN-FAMILY:IPR015365 , InterPro:IN-FAMILY:IPR020599 , PDB:Structure:3A5Z , Pfam:IN-FAMILY:PF01132 , Pfam:IN-FAMILY:PF08207 , Pfam:IN-FAMILY:PF09285 , Prosite:IN-FAMILY:PS01275 , Smart:IN-FAMILY:SM00841

In Paralogous Gene Group: 386 (2 members)

In Reactions of unknown directionality:

Not in pathways:
protein chain elongation factor EF-P + (R)-β-lysine + ATP = protein chain elongation factor EF-P, β-lysyl-Lys34 + AMP + diphosphate

GO Terms:

Biological Process: GO:0006414 - translational elongation Inferred from experiment Inferred by computational analysis [UniProtGOA12, UniProtGOA11a, GOA06, GOA01a, Doerfel13, Ude13]
GO:0006412 - translation Inferred by computational analysis [UniProtGOA11a]
GO:0043043 - peptide biosynthetic process Inferred by computational analysis [GOA01a]
Molecular Function: GO:0003746 - translation elongation factor activity Inferred from experiment Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a, Ude13, Doerfel13, Glick75]
GO:0043022 - ribosome binding Inferred from experiment [Aoki08a]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06, GOA01a, Glick75]
GO:0005829 - cytosol Inferred from experiment [Glick75]

MultiFun Terms: information transfer protein related translation

Essentiality data for efp knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Citations Growth Observations
LB Lennox Low 37 Aerobic 7   [Yanagisawa10] No [Aoki97a]
Yes [Baba06, Comment 1]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35   Yes [Joyce06, Comment 2]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22   Yes [Baba06, Comment 1]

Last-Curated ? 25-Mar-2015 by Keseler I , SRI International

Sequence Features

Protein sequence of protein chain elongation factor EF-P with features indicated

Feature Class Location Common Name Citations Comment State
Cleavage-of-Initial-Methionine 1  
[Aoki91, Link97, UniProt11a, Aoki91]
UniProt: Removed.
Chain 2 -> 188  
UniProt: Elongation factor P;
Mutagenesis-Variant 31  
[Yanagisawa10, UniProt12b]
UniProt: No lysylation.
Mutagenesis-Variant 33  
[Yanagisawa10, UniProt12b]
UniProt: No lysylation. Loss of in vivo EF-P function for cell growth.
Mutagenesis-Variant 34  
[Yanagisawa10, Park12, Ude13, UniProt13]
UniProt: No lysylation and loss of EF-P activity. No facilitation of translation of poly-Pro stretches.
Modified-Residue 34 β-lysyl-lysine
[Park12, Roy11, Peil12, Yanagisawa10, Park12, Roy11]

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b4147 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12099; confirmed by SwissProt match.


An80: An G, Glick BR, Friesen JD, Ganoza MC (1980). "Identification and quantitation of elongation factor EF-P in Escherichia coli cell-free extracts." Can J Biochem 58(11);1312-4. PMID: 7011506

Aoki02: Aoki H, Ke L, Poppe SM, Poel TJ, Weaver EA, Gadwood RC, Thomas RC, Shinabarger DL, Ganoza MC (2002). "Oxazolidinone antibiotics target the P site on Escherichia coli ribosomes." Antimicrob Agents Chemother 46(4);1080-5. PMID: 11897593

Aoki08a: Aoki H, Xu J, Emili A, Chosay JG, Golshani A, Ganoza MC (2008). "Interactions of elongation factor EF-P with the Escherichia coli ribosome." FEBS J 275(4);671-81. PMID: 18201202

Aoki91: Aoki H, Adams SL, Chung DG, Yaguchi M, Chuang SE, Ganoza MC (1991). "Cloning, sequencing and overexpression of the gene for prokaryotic factor EF-P involved in peptide bond synthesis." Nucleic Acids Res 1991;19(22);6215-20. PMID: 1956781

Aoki97: Aoki H, Adams SL, Turner MA, Ganoza MC (1997). "Molecular characterization of the prokaryotic efp gene product involved in a peptidyltransferase reaction." Biochimie 79(1);7-11. PMID: 9195040

Aoki97a: Aoki H, Dekany K, Adams SL, Ganoza MC (1997). "The gene encoding the elongation factor P protein is essential for viability and is required for protein synthesis." J Biol Chem 272(51);32254-9. PMID: 9405429

Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bailly10: Bailly M, de Crecy-Lagard V (2010). "Predicting the pathway involved in post-translational modification of Elongation factor P in a subset of bacterial species." Biol Direct 5(1);3. PMID: 20070887

Balibar13: Balibar CJ, Iwanowicz D, Dean CR (2013). "Elongation factor P is dispensable in Escherichia coli and Pseudomonas aeruginosa." Curr Microbiol 67(3);293-9. PMID: 23591475

Baxter87: Baxter RM, Ganoza MC, Zahid N, Chung DG (1987). "Reconstruction of peptidyltransferase activity on 50S and 70S ribosomal particles by peptide fragments of protein L16." Eur J Biochem 163(3);473-9. PMID: 3549294

Blaha09: Blaha G, Stanley RE, Steitz TA (2009). "Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome." Science 325(5943);966-70. PMID: 19696344

Bullwinkle13: Bullwinkle TJ, Zou SB, Rajkovic A, Hersch SJ, Elgamal S, Robinson N, Smil D, Bolshan Y, Navarre WW, Ibba M (2013). "(R)-β-Lysine-modified Elongation Factor P Functions in Translation Elongation." J Biol Chem 288(6);4416-23. PMID: 23277358

Buskirk13: Buskirk AR, Green R (2013). "Biochemistry. Getting past polyproline pauses." Science 339(6115);38-9. PMID: 23288527

Doerfel13: Doerfel LK, Wohlgemuth I, Kothe C, Peske F, Urlaub H, Rodnina MV (2013). "EF-P is essential for rapid synthesis of proteins containing consecutive proline residues." Science 339(6115);85-8. PMID: 23239624

Elgamal14: Elgamal S, Katz A, Hersch SJ, Newsom D, White P, Navarre WW, Ibba M (2014). "EF-P dependent pauses integrate proximal and distal signals during translation." PLoS Genet 10(8);e1004553. PMID: 25144653

Ganoza00: Ganoza MC, Aoki H (2000). "Peptide bond synthesis: function of the efp gene product." Biol Chem 381(7);553-9. PMID: 10987361

Ganoza85: Ganoza MC, Zahid N, Baxter RM (1985). "Stimulation of peptidyltransferase reactions by a soluble protein." Eur J Biochem 146(2);287-94. PMID: 3881259

Glick75: Glick BR, Ganoza MC (1975). "Identification of a soluble protein that stimulates peptide bond synthesis." Proc Natl Acad Sci U S A 72(11);4257-60. PMID: 1105576

Glick76: Glick BR, Ganoza MC (1976). "Characterization and site of action of a soluble protein that stimulates peptide-bond synthesis." Eur J Biochem 71(2);483-91. PMID: 795670

Glick79: Glick BR, Chladek S, Ganoza MC (1979). "Peptide bond formation stimulated by protein synthesis factor EF-P depends on the aminoacyl moiety of the acceptor." Eur J Biochem 97(1);23-8. PMID: 383483

Glick79a: Glick BR, Green RM, Ganoza MC (1979). "Purification and Best Department of Medical Research, University of Toronto, Ont., Canada." Can J Biochem 57(6);749-57. PMID: 383236

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Green85: Green RH, Glick BR, Ganoza MC (1985). "Requirements for in vitro reconstruction of protein synthesis." Biochem Biophys Res Commun 126(2);792-8. PMID: 3884000

Hersch13: Hersch SJ, Wang M, Zou SB, Moon KM, Foster LJ, Ibba M, Navarre WW (2013). "Divergent Protein Motifs Direct Elongation Factor P-Mediated Translational Regulation in Salmonella enterica and Escherichia coli." MBio 4(2). PMID: 23611909

Hersch14: Hersch SJ, Elgamal S, Katz A, Ibba M, Navarre WW (2014). "Translation initiation rate determines the impact of ribosome stalling on bacterial protein synthesis." J Biol Chem 289(41);28160-71. PMID: 25148683

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Link97: Link AJ, Robison K, Church GM (1997). "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12." Electrophoresis 18(8);1259-313. PMID: 9298646

Mandal14: Mandal A, Mandal S, Park MH (2014). "Genome-wide analyses and functional classification of proline repeat-rich proteins: potential role of eIF5A in eukaryotic evolution." PLoS One 9(11);e111800. PMID: 25364902

Park12: Park JH, Johansson HE, Aoki H, Huang BX, Kim HY, Ganoza MC, Park MH (2012). "Post-translational modification by β-lysylation is required for activity of Escherichia coli elongation factor P (EF-P)." J Biol Chem 287(4);2579-90. PMID: 22128152

Peil12: Peil L, Starosta AL, Virumae K, Atkinson GC, Tenson T, Remme J, Wilson DN (2012). "Lys34 of translation elongation factor EF-P is hydroxylated by YfcM." Nat Chem Biol 8(8);695-7. PMID: 22706199

Peil13: Peil L, Starosta AL, Lassak J, Atkinson GC, Virumae K, Spitzer M, Tenson T, Jung K, Remme J, Wilson DN (2013). "Distinct XPPX sequence motifs induce ribosome stalling, which is rescued by the translation elongation factor EF-P." Proc Natl Acad Sci U S A 110(38);15265-70. PMID: 24003132

Robertson94: Robertson ES, Aggison LA, Nicholson AW (1994). "Phosphorylation of elongation factor G and ribosomal protein S6 in bacteriophage T7-infected Escherichia coli." Mol Microbiol 11(6);1045-57. PMID: 8022276

Roy11: Roy H, Zou SB, Bullwinkle TJ, Wolfe BS, Gilreath MS, Forsyth CJ, Navarre WW, Ibba M (2011). "The tRNA synthetase paralog PoxA modifies elongation factor-P with (R)-β-lysine." Nat Chem Biol 7(10);667-9. PMID: 21841797

Starosta14: Starosta AL, Lassak J, Peil L, Atkinson GC, Virumae K, Tenson T, Remme J, Jung K, Wilson DN (2014). "Translational stalling at polyproline stretches is modulated by the sequence context upstream of the stall site." Nucleic Acids Res 42(16);10711-9. PMID: 25143529

Starosta14a: Starosta AL, Lassak J, Peil L, Atkinson GC, Woolstenhulme CJ, Virumae K, Buskirk A, Tenson T, Remme J, Jung K, Wilson DN (2014). "A conserved proline triplet in Val-tRNA synthetase and the origin of elongation factor P." Cell Rep 9(2);476-83. PMID: 25310979

Sumida10: Sumida T, Yanagisawa T, Ishii R, Yokoyama S (2010). "Crystallization and preliminary X-ray crystallographic study of GenX, a lysyl-tRNA synthetase paralogue from Escherichia coli, in complex with translation elongation factor P." Acta Crystallogr Sect F Struct Biol Cryst Commun 66(Pt 9);1115-8. PMID: 20823541

Ude13: Ude S, Lassak J, Starosta AL, Kraxenberger T, Wilson DN, Jung K (2013). "Translation elongation factor EF-P alleviates ribosome stalling at polyproline stretches." Science 339(6115);82-5. PMID: 23239623

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt11a: UniProt Consortium (2011). "UniProt version 2011-06 released on 2011-06-30 00:00:00." Database.

UniProt12b: UniProt Consortium (2012). "UniProt version 2012-11 released on 2012-11-26 00:00:00." Database.

UniProt13: UniProt Consortium (2013). "UniProt version 2013-08 released on 2013-08-01 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

UniProtGOA12: UniProt-GOA (2012). "Gene Ontology annotation based on UniPathway vocabulary mapping."

Woolstenhulme13: Woolstenhulme CJ, Parajuli S, Healey DW, Valverde DP, Petersen EN, Starosta AL, Guydosh NR, Johnson WE, Wilson DN, Buskirk AR (2013). "Nascent peptides that block protein synthesis in bacteria." Proc Natl Acad Sci U S A 110(10);E878-87. PMID: 23431150

Yanagisawa10: Yanagisawa T, Sumida T, Ishii R, Takemoto C, Yokoyama S (2010). "A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P." Nat Struct Mol Biol 17(9);1136-43. PMID: 20729861

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Sat Oct 3, 2015, biocyc13.