Escherichia coli K-12 substr. MG1655 Enzyme: EF-P-lysine lysyltransferase

Gene: epmA Accession Numbers: EG11211 (EcoCyc), b4155, ECK4151

Synonyms: genX, poxA, yjeA

Regulation Summary Diagram: ?

Regulation summary diagram for epmA

Subunit composition of EF-P-lysine lysyltransferase = [EpmA]2
         EF-P-lysine lysyltransferase = EpmA

EpmA specifically aminoacylates the protein chain elongation factor EF-P at the ε-amino group of Lys34 with lysine [Yanagisawa10]. EF-P is a structural mimic of tRNA; it appears to be the only cellular target for lysylation by EpmA [Park12]. Site-directed mutagenesis identified residues within EpmA that are critical for activity, and residues within EF-P that are critical for its ability to be modified. Co-expression of EpmB enhances the lysylation of EF-P by EpmA in vivo [Yanagisawa10, Park12].

EpmA has sequence similarity to the class II LysRS tRNA aminoacyltransferase, but lacks the anticodon binding domain. The enzyme is able to catalyze ATP-dependent activation of lysine and lysine analogs by formation of a lysine adenylate [Ambrogelly10]; (R)-β-lysine is the most efficient substrate [Roy11].

EpmA was originally suggested to regulate pyruvate oxidase and named PoxA. The pyruvate oxidase activity of a epmA mutant is severalfold decreased compared to wild type [Chang82]. An epmA mutant shows pleiotropic phenotypes (including drug sensitivities) distinct from the phenotypes of a poxB mutant, which lacks pyruvate oxidase [Van87].

A structural alignment [Bailly10] and crystal structure [Yanagisawa10] shows that EpmA has similarity to the catalytic core of the class II lysyl-tRNA synthetase, but lacking the tRNA anticodon binding domain. Physical clustering and phylogenetic analysis have implicated EpmA in a pathway for the modification of a lysine residue in protein chain elongation factor EF-P [Bailly10].

EpmA: "EF-P post-translational modification A" [Peil12]

Citations: [Sumida10]

Locations: cytosol

Map Position: [4,380,666 -> 4,381,643] (94.42 centisomes, 340°)
Length: 978 bp / 325 aa

Molecular Weight of Polypeptide: 36.976 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0013610 , DIP:DIP-10535N , EchoBASE:EB1196 , EcoGene:EG11211 , EcoliWiki:b4155 , ModBase:P0A8N7 , OU-Microarray:b4155 , PortEco:poxA , Pride:P0A8N7 , Protein Model Portal:P0A8N7 , RefSeq:NP_418579 , RegulonDB:EG11211 , SMR:P0A8N7 , String:511145.b4155 , UniProt:P0A8N7

Relationship Links: InterPro:IN-FAMILY:IPR004364 , InterPro:IN-FAMILY:IPR004525 , InterPro:IN-FAMILY:IPR006195 , InterPro:IN-FAMILY:IPR018149 , InterPro:IN-FAMILY:IPR018150 , Panther:IN-FAMILY:PTHR22594 , Panther:IN-FAMILY:PTHR22594:SF7 , PDB:PART-OF:3A5Z , PDB:Structure:3A5Y , Pfam:IN-FAMILY:PF00152 , Prints:IN-FAMILY:PR00982 , Prosite:IN-FAMILY:PS50862

In Paralogous Gene Group: 575 (3 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0071915 - protein-lysine lysylation Inferred from experiment Inferred by computational analysis [GOA06, Yanagisawa10]
GO:0072581 - protein-N6-(L-lysyl)-L-lysine modification to protein-N6-(beta-lysyl)-L-lysine Inferred from experiment [Park12]
GO:0006418 - tRNA aminoacylation for protein translation Inferred by computational analysis [GOA01a]
GO:0006430 - lysyl-tRNA aminoacylation Inferred by computational analysis [GOA01a]
GO:0043687 - post-translational protein modification Inferred by computational analysis [Bailly10]
Molecular Function: GO:0052868 - protein-lysine lysyltransferase activity Inferred from experiment [Yanagisawa10]
GO:0000166 - nucleotide binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0004812 - aminoacyl-tRNA ligase activity Inferred by computational analysis [GOA01a]
GO:0004824 - lysine-tRNA ligase activity Inferred by computational analysis [GOA01a]
GO:0005524 - ATP binding Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
GO:0016874 - ligase activity Inferred by computational analysis [UniProtGOA11a]
GO:0016880 - acid-ammonia (or amide) ligase activity Inferred by computational analysis [GOA06]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08]
GO:0005737 - cytoplasm Inferred by computational analysis [GOA01a]

MultiFun Terms: regulation type of regulation posttranscriptional covalent modification, demodification, maturation

Essentiality data for epmA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB Lennox Yes 37 Aerobic 7   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]

Created 03-Sep-2010 by Keseler I , SRI International
Last-Curated ? 15-Dec-2011 by Keseler I , SRI International

Enzymatic reaction of: EF-P-lysine lysyltransferase

protein chain elongation factor EF-P + (R)-β-lysine + ATP <=> protein chain elongation factor EF-P, β-lysyl-Lys34 + AMP + diphosphate

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

Reversibility of this reaction is unspecified.

a [protein chain elongation factor EF-P]-L-lysine34 + (R)-β-lysine + ATP <=> [a protein chain elongation factor EF-P]-β-L-lysyl-L-lysine34 + AMP + diphosphate + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

At a low concentration of lysine, the enzyme has a pH optimum between 9 and10; however, at higher lysine concentration, the reaction rate is similar between pH7.5 and 10 [Park12].

Activators (Unknown Mechanism): Mg2+ [Ambrogelly10]

Kinetic Parameters:

Km (μM)

pH(opt): 7.5-10 [Park12]

Sequence Features

Protein sequence of EF-P-lysine lysyltransferase with features indicated

Feature Class Location Attached Group Citations Comment
Mutagenesis-Variant 50  
[Yanagisawa10, UniProt12b]
UniProt: No effect on lysylation activity.
Mutagenesis-Variant 76  
[Roy11, UniProt12b]
UniProt: Loss of catalytic activity.
Protein-Segment 76 -> 78  
UniProt: Substrate binding; Sequence Annotation Type: region of interest.
Sequence-Conflict 78  
[Cole82a, UniProt10a]
UniProt: (in Ref. 5; AAA23436);
Nucleotide-Phosphate-Binding-Region 100 -> 102 ATP
UniProt: ATP.
Mutagenesis-Variant 100  
[Yanagisawa10, UniProt12b]
UniProt: Loss of lysylation activity.
Mutagenesis-Variant 102  
[Yanagisawa10, UniProt12b]
UniProt: No effect on lysylation activity.
Mutagenesis-Variant 103  
[Yanagisawa10, UniProt12b]
UniProt: Loss of lysylation activity.
Mutagenesis-Variant 108  
[Yanagisawa10, UniProt12b]
UniProt: Severe reduction in lysylation activity.
Amino-Acid-Sites-That-Bind 109  
UniProt: ATP; via amide nitrogen and carbonyl oxygen.
Amino-Acid-Sites-That-Bind 118  
UniProt: Substrate.
Sequence-Conflict 144  
[Cole82a, UniProt10a]
UniProt: (in Ref. 5; AAA23436);
Mutagenesis-Variant 185  
[Yanagisawa10, UniProt12b]
UniProt: Slight reduction in lysylation activity.
Mutagenesis-Variant 193  
[Yanagisawa10, UniProt12b]
UniProt: Slight reduction in lysylation activity.
Nucleotide-Phosphate-Binding-Region 244 -> 245 ATP
UniProt: ATP.
Mutagenesis-Variant 244  
[Yanagisawa10, UniProt12b]
UniProt: Loss of lysylation activity.
Mutagenesis-Variant 247  
[Yanagisawa10, UniProt12b]
UniProt: Loss of lysylation activity.
Amino-Acid-Sites-That-Bind 251  
UniProt: Substrate.
Mutagenesis-Variant 298  
[Roy11, UniProt12b]
UniProt: 96% increase in the affinity for L- alpha-lysine. 4-fold decrease in the catalytic efficiency of the (R)-beta- lysine activation reaction.
Amino-Acid-Sites-That-Bind 300  
UniProt: ATP; via amide nitrogen.
Mutagenesis-Variant 303  
[Yanagisawa10, UniProt12b]
UniProt: Loss of lysylation activity.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Peter D. Karp on Wed Jan 18, 2006:
Gene left-end position adjusted based on analysis performed in the 2005 E. coli annotation update [Riley06 ].
10/20/97 Gene b4155 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11211; confirmed by SwissProt match.


Ambrogelly10: Ambrogelly A, O'Donoghue P, Soll D, Moses S (2010). "A bacterial ortholog of class II lysyl-tRNA synthetase activates lysine." FEBS Lett 584(14);3055-60. PMID: 20580719

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

Chang82: Chang YY, Cronan JE (1982). "Mapping nonselectable genes of Escherichia coli by using transposon Tn10: location of a gene affecting pyruvate oxidase." J Bacteriol 151(3);1279-89. PMID: 6286595

Cole82a: Cole ST (1982). "Nucleotide sequence coding for the flavoprotein subunit of the fumarate reductase of Escherichia coli." Eur J Biochem 122(3);479-84. PMID: 7037404

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

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."

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

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

Riley06: Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL (2006). "Escherichia coli K-12: a cooperatively developed annotation snapshot--2005." Nucleic Acids Res 34(1);1-9. PMID: 16397293

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

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-11 released on 2010-11-02 00:00:00." Database.

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

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

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

Van87: Van Dyk TK, Smulski DR, Chang YY (1987). "Pleiotropic effects of poxA regulatory mutations of Escherichia coli and Salmonella typhimurium, mutations conferring sulfometuron methyl and alpha-ketobutyrate hypersensitivity." J Bacteriol 169(10);4540-6. PMID: 2820932

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

Other References Related to Gene Regulation

MendozaVargas09: Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juarez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009). "Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli." PLoS One 4(10);e7526. PMID: 19838305

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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