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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: ?

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

Summary:
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]. The EF-P binding site on the ribosome overlaps the peptidyltransferase center [Aoki97]; interactions between EF-P and 70S ribosomes have been mapped [Aoki08]. It was previously thought that EF-P might facilitate proper positioning of fMet-tRNAfMet for initial peptide bond formation [Aoki08, 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].

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]. An efp deletion strain 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 [Aoki08], 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]

Locations: cytosol

Map Position: [4,373,722 -> 4,374,288] (94.27 centisomes)
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 + D-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, UniProtGOA11, GOA06, GOA01, Doerfel13, Ude13]
GO:0006412 - translation Inferred by computational analysis [UniProtGOA11]
GO:0043043 - peptide biosynthetic process Inferred by computational analysis [GOA01]
Molecular Function: GO:0003746 - translation elongation factor activity Inferred from experiment Inferred by computational analysis [UniProtGOA11, GOA06, GOA01, Ude13, Doerfel13, Glick75]
GO:0043022 - ribosome binding Inferred from experiment [Aoki08]
Cellular Component: GO:0005737 - cytoplasm Inferred from experiment Inferred by computational analysis [UniProtGOA11a, UniProtGOA11, GOA06, GOA01, 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] Yes [Baba06, Comment 1]
No [Aoki97a]
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]

Credits:
Last-Curated ? 30-Apr-2013 by Keseler I , SRI International


Sequence Features

Feature Class Location Common Name Citations Comment State
Cleavage-of-Initial-Methionine 1  
[Aoki91, Link97, UniProt11a, Aoki91]
UniProt: Removed.
 
Chain 2 -> 188  
[UniProt09]
UniProt: Elongation factor P;
 
Mutagenesis-Variant 31  
[Yanagisawa10, UniProt12]
Alternate sequence: K → A; UniProt: No lysylation.
 
Mutagenesis-Variant 33  
[Yanagisawa10, UniProt12]
Alternate sequence: G → K; UniProt: No lysylation. Loss of in vivo EF-P function for cell growth.
 
Mutagenesis-Variant 34  
[Yanagisawa10, Park12, Ude13, UniProt13]
Alternate sequence: K → A; UniProt: No lysylation and loss of EF-P activity. No facilitation of translation of poly-Pro stretches.
 
Modified-Residue 34 β-lysyl-lysine
[Peil12, Yanagisawa10, Park12, Roy11]
  Modified


Gene Local Context (not to scale): ?

Transcription Unit:

Notes:

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


References

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

Aoki08: 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. 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

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

GOA01: 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

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

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

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

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.

UniProt12: 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 manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

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

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

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 18.5 on Wed Nov 26, 2014, biocyc11.