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Gene Review

epmA  -  Elongation Factor P Lys34 lysyltransferase

Escherichia coli str. K-12 substr. MG1655

Synonyms: ECK4151, JW4116, genX, poxA, yjeA
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Disease relevance of poxA

  • Using a Tn10 insertion greater than 98% cotransduced with the poxA locus, we mapped the poxA gene on the E. coli genetic map [1].
  • The crystal structures of Thermus thermophilus lysyl-tRNA synthetase, a class IIb aminoacyl-tRNA synthetase, complexed with Escherchia coli tRNA(Lys)(mnm5 s2UUU) at 2.75 A resolution and with a T. thermophilus tRNA(Lys)(CUU) transcript at 2.9 A resolution are described [2].
  • Three Trp variants of lysyl-tRNA synthetase from Bacillus stearothermophilus, in which either one or both of the two Trp residues within the enzyme (Trp314 and Trp332) were substituted by a Phe residue, were produced by site-directed mutagenesis without appreciable loss of catalytic activity [3].
  • However, the capacity of tRNA(3)(Lys) to interact with lysyl-tRNA synthetase does not entirely explain the enhanced preference for selection of tRNA(3)(Lys) for the replication of HIV-1 [4].
  • The relationship of the pleiotropic phenotypes of the poxA mutants to their SM hypersensitivity is discussed [5].

High impact information on poxA

  • Multiple control of Escherichia coli lysyl-tRNA synthetase expression involves a transcriptional repressor and a translational enhancer element [6].
  • Searches of the current protein banks also have revealed a high degree of sequence similarity of the lysyl-tRNA synthetase to the product of the Escherichia coli herC gene and to the partial sequence of a protein encoded by an unidentified reading frame located adjacent to the E. coli frdA gene [7].
  • In the presence of purified Escherichia coli lysyl-tRNA synthetase [L-lysine:tRNALys ligase (AMP-forming) EC], L-lysine, and ATP, addition of the nucleotide ppGpp results in formation of a unique product-A(5')ppp(5') Gpp [8].
  • Upon the addition of 3 mM L-leucyl-L-alanine to the medium the lysyl tRNA synthetase activity increases 25-fold and the in vivo charging of lysine tRNA returns to the wild-type level [9].
  • To compare amino acid recognition between the two forms of LysRS, the effects of l-lysine analogues on aminoacylation were investigated [10].

Chemical compound and disease context of poxA


Biological context of poxA

  • To map this nonselectable mutation, we isolated strains having transposon Tn10 inserted into the chromosome close to the poxA locus and mapped the transposon [1].
  • Loss of this base pair reduces mischarging by the E. coli lysyl-tRNA synthetase [14].
  • In the present study, the specificity of constitutive lysyl-tRNA synthetase (LysS) from Escherichia coli was analyzed by cross-mutagenesis of the tRNA(Lys) anticodon, on the one hand, and of the amino acid residues composing the anticodon binding site on the other [15].
  • A protein domain corresponding to residues 31 to 149 of the E. coli Lysyl-tRNA synthetase species corresponding to the lysS gene was expressed and 15N-labelled [16].
  • Therefore, the behavior of the Thr 208 mutants of LysRS supports the idea that the dimerization of class II aminoacyl-tRNA synthetases is important for an efficient structuration of their active site [11].

Anatomical context of poxA

  • Lysinoalanine [N epsilon-(DL-2-amino-2-carboxyethyl)-L-lysine; LAL], a nephrotoxic lysine analog, inhibits the lysyl-tRNA-synthetase (EC of prokaryotic and eukaryotic cells competitively at micromolar concentrations [17].

Associations of poxA with chemical compounds

  • One of these lesions (designated poxA) decreased the pyruvate oxidase activity to 10 to 15% of the normal level but grew well [1].
  • Lysine insertion during coded protein synthesis requires lysyl-tRNA(Lys), which is synthesized by lysyl-tRNA synthetase (LysRS) [10].
  • T208A LysRS, in which threonine 208 had been changed into alanine by site-directed mutagenesis, displayed the same properties as T208M LysRS [11].
  • The heterogeneity of lysyl-tRNA synthetase (LysRS) was revealed on hydroxyapatite; we focused on the first peak, LysRS1, because of its higher Ap4A/lysyl-tRNA activity ratio at that stage [13].
  • The folate operon contains two promoters, one upstream of the first gene and the second preceding LysS [18].

Other interactions of poxA


Analytical, diagnostic and therapeutic context of poxA


  1. Mapping nonselectable genes of Escherichia coli by using transposon Tn10: location of a gene affecting pyruvate oxidase. Chang, Y.Y., Cronan, J.E. J. Bacteriol. (1982) [Pubmed]
  2. The crystal structures of T. thermophilus lysyl-tRNA synthetase complexed with E. coli tRNA(Lys) and a T. thermophilus tRNA(Lys) transcript: anticodon recognition and conformational changes upon binding of a lysyl-adenylate analogue. Cusack, S., Yaremchuk, A., Tukalo, M. EMBO J. (1996) [Pubmed]
  3. Lysyl-tRNA synthetase from Bacillus stearothermophilus: the Trp314 residue is shielded in a non-polar environment and is responsible for the fluorescence changes observed in the amino acid activation reaction. Takita, T., Nakagoshi, M., Inouye, K., Tonomura, B. J. Mol. Biol. (2003) [Pubmed]
  4. Complementation of Human Immunodeficiency Virus Type 1 Replication by Intracellular Selection of Escherichia coli Formula Supplied in trans. McCulley, A., Morrow, C.D. J. Virol. (2006) [Pubmed]
  5. Pleiotropic effects of poxA regulatory mutations of Escherichia coli and Salmonella typhimurium, mutations conferring sulfometuron methyl and alpha-ketobutyrate hypersensitivity. Van Dyk, T.K., Smulski, D.R., Chang, Y.Y. J. Bacteriol. (1987) [Pubmed]
  6. Multiple control of Escherichia coli lysyl-tRNA synthetase expression involves a transcriptional repressor and a translational enhancer element. Ito, K., Kawakami, K., Nakamura, Y. Proc. Natl. Acad. Sci. U.S.A. (1993) [Pubmed]
  7. Homology of aspartyl- and lysyl-tRNA synthetases. Gampel, A., Tzagoloff, A. Proc. Natl. Acad. Sci. U.S.A. (1989) [Pubmed]
  8. Relationship of the first step in protein synthesis to ppGpp: formation of A(5')ppp(5')Gpp. Rapaport, E., Svihovec, S.K., Zamecnik, P.C. Proc. Natl. Acad. Sci. U.S.A. (1975) [Pubmed]
  9. Metabolites influence control of lysine transfer ribonucleic acid synthetase formation in Escherichia coli K-12. Hirshfield, I.N., Yeh, F.M., Sawyer, L.E. Proc. Natl. Acad. Sci. U.S.A. (1975) [Pubmed]
  10. Divergence in noncognate amino acid recognition between class I and class II lysyl-tRNA synthetases. Levengood, J., Ataide, S.F., Roy, H., Ibba, M. J. Biol. Chem. (2004) [Pubmed]
  11. A single substitution in the motif 1 of Escherichia coli lysyl-tRNA synthetase induces cooperativity toward amino acid binding. Commans, S., Blanquet, S., Plateau, P. Biochemistry (1995) [Pubmed]
  12. Active site of lysyl-tRNA synthetase: structural studies of the adenylation reaction. Desogus, G., Todone, F., Brick, P., Onesti, S. Biochemistry (2000) [Pubmed]
  13. Lysyl-tRNA synthetase from Escherichia coli K12. Chromatographic heterogeneity and the lysU-gene product. Charlier, J., Sanchez, R. Biochem. J. (1987) [Pubmed]
  14. Design of a bacterial host for site-specific incorporation of p-bromophenylalanine into recombinant proteins. Kwon, I., Wang, P., Tirrell, D.A. J. Am. Chem. Soc. (2006) [Pubmed]
  15. tRNA anticodon recognition and specification within subclass IIb aminoacyl-tRNA synthetases. Commans, S., Lazard, M., Delort, F., Blanquet, S., Plateau, P. J. Mol. Biol. (1998) [Pubmed]
  16. Solution structure of the anticodon-binding domain of Escherichia coli lysyl-tRNA synthetase and studies of its interaction with tRNA(Lys). Commans, S., Plateau, P., Blanquet, S., Dardel, F. J. Mol. Biol. (1995) [Pubmed]
  17. Interaction of lysinoalanine with the protein synthesizing apparatus. Lifsey, B.J., Farkas, W.R., Reyniers, J.P. Chem. Biol. Interact. (1988) [Pubmed]
  18. The trp RNA-binding attenuation protein (TRAP) regulates the steady-state levels of transcripts of the Bacillus subtilis folate operon. de Saizieu, A., Vankan, P., Vockler, C., van Loon, A.P. Microbiology (Reading, Engl.) (1997) [Pubmed]
  19. Homology of lysS and lysU, the two Escherichia coli genes encoding distinct lysyl-tRNA synthetase species. Lévêque, F., Plateau, P., Dessen, P., Blanquet, S. Nucleic Acids Res. (1990) [Pubmed]
  20. Anticodon recognition in evolution: switching tRNA specificity of an aminoacyl-tRNA synthetase by site-directed peptide transplantation. Brevet, A., Chen, J., Commans, S., Lazennec, C., Blanquet, S., Plateau, P. J. Biol. Chem. (2003) [Pubmed]
  21. Crystallization and preliminary diffraction studies of Escherichia coli lysyl-tRNA synthetase (LysU). Onesti, S., Theoclitou, M.E., Pernilla, E., Wittung, L., Miller, A.D., Plateau, P., Blanquet, S., Brick, P. J. Mol. Biol. (1994) [Pubmed]
  22. Escherichia coli K-12 lysyl-tRNA synthetase mutant with a novel reversion pattern. Hirshfield, I.N., Tenreiro, R., Vanbogelen, R.A., Neidhardt, F.C. J. Bacteriol. (1984) [Pubmed]
  23. Misacylation of Yeast Amber Suppressor tRNATyr by E. coli Lysyl-tRNA Synthetase and Its Effective Repression by Genetic Engineering of the tRNA Sequence. Fukunaga, J., Yokogawa, T., Ohno, S., Nishikawa, K. J. Biochem. (2006) [Pubmed]
  24. Lysyl-tRNA synthetase of Bacillus stearothermophilus molecular cloning and expression of the gene. Takita, T., Shimizu, N., Sukata, T., Hashimoto, S., Akita, E., Yokota, T., Esaki, N., Soda, K., Inouye, K., Tonomura, B. Biosci. Biotechnol. Biochem. (2000) [Pubmed]
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