title: Structural elements defining elongation factor Tu mediated suppression of codon ambiguity.
abstract: In most prokaryotes Asn-tRNA(Asn) and Gln-tRNA(Gln) are formed by amidation of aspartate and glutamate mischarged onto tRNA(Asn) and tRNA(Gln), respectively. Coexistence in the organism of mischarged Asp-tRNA(Asn) and Glu-tRNA(Gln) and the homologous Asn-tRNA(Asn) and Gln-tRNA(Gln) does not, however, lead to erroneous incorporation of Asp and Glu into proteins, since EF-Tu discriminates the misacylated tRNAs from the correctly charged ones. This property contrasts with the canonical function of EF-Tu, which is to non-specifically bind the homologous aa-tRNAs, as well as heterologous species formed in vitro by aminoacylation of non-cognate tRNAs. In Thermus thermophilus that forms the Asp-tRNA(Asn) intermediate by the indirect pathway of tRNA asparaginylation, EF-Tu must discriminate the mischarged aminoacyl-tRNAs (aa-tRNA). We show that two base pairs in the tRNA T-arm and a single residue in the amino acid binding pocket of EF-Tu promote discrimination of Asp-tRNA(Asn) from Asn-tRNA(Asn) and Asp-tRNA(Asp) by the protein. Our analysis suggests that these structural elements might also contribute to rejection of other mischarged aa-tRNAs formed in vivo that are not involved in peptide elongation. Additionally, these structural features might be involved in maintaining a delicate balance of weak and strong binding affinities between EF-Tu and the amino acid and tRNA moieties of other elongator aa-tRNAs.
authors.affiliation: UPR 9002, Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, 15, Rue René Descartes and Université Louis Pasteur, F-67084 Strasbourg Cédex, France.
authors.forename: Hervé
authors.initials: H
authors.lastname: Roy
authors.forename: Hubert Dominique
authors.initials: HD
authors.lastname: Becker
authors.forename: Marie-Hélène
authors.initials: MH
authors.lastname: Mazauric
authors.forename: Daniel
authors.initials: D
authors.lastname: Kern
mesh_terms: D020029:Base Pairing; D003062:Codon; D029968:Escherichia coli Proteins / Q000378:metabolism; D008958:Models, Molecular; D010444:Peptide Elongation Factor Tu / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D012346:RNA, Transfer, Amino Acyl / Q000737:chemistry* / Q000378:metabolism; D012348:RNA, Transfer, Asn / Q000737:chemistry* / Q000378:metabolism; D012349:RNA, Transfer, Asp / Q000737:chemistry / Q000378:metabolism; D016963:Thermus thermophilus / Q000235:genetics; D046249:Transfer RNA Aminoacylation
chemical_list: D003062:Codon; D029968:Escherichia coli Proteins; D012346:RNA, Transfer, Amino Acyl; D012348:RNA, Transfer, Asn; D012349:RNA, Transfer, Asp; D010444:Peptide Elongation Factor Tu