title: Universal pathway for posttransfer editing reactions: insights from the crystal structure of TtPheRS with puromycin.
abstract: At the amino acid binding and recognition step, phenylalanyl-tRNA synthetase (PheRS) faces the challenge of discrimination between cognate phenylalanine and closely similar noncognate tyrosine. Resampling of Tyr-tRNA(Phe) to PheRS increasing the number of correctly charged tRNA molecules has recently been revealed. Thus, the very same editing site of PheRS promotes hydrolysis of misacylated tRNA species, associated both with cis- and trans-editing pathways. Here we report the crystal structure of Thermus thermophilus PheRS (TtPheRS) at 2.6 Å resolution, in complex with phenylalanine and antibiotic puromycin mimicking the A76 of tRNA acylated with tyrosine. Starting from the complex structure and using a hybrid quantum mechanics/molecular mechanics approach, we investigate the pathways of editing reaction catalyzed by TtPheRS. We show that both 2' and 3' isomeric esters undergo mutual transformation via the cyclic intermediate orthoester, and the editing site can readily accommodate a model of Tyr-tRNA(Phe) where deacylation occurs from either the 2'- or 3'-OH. The suggested pathway of the hydrolytic reaction at the editing site of PheRS is of sufficient generality to warrant comparison with other class I and class II aminoacyl-tRNA synthetases.
authors.affiliation: Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel;
authors.forename: Dmitry
authors.initials: D
authors.lastname: Tworowski
authors.affiliation: Medical Research Council, Mitochondrial Biology Unit, Cambridge CB2 0XY, United Kingdom; and.
authors.forename: Liron
authors.initials: L
authors.lastname: Klipcan
authors.affiliation: Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel;
authors.forename: Moshe
authors.initials: M
authors.lastname: Peretz
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine, 630090 Novosibirsk, Russia.
authors.forename: Nina
authors.initials: N
authors.lastname: Moor
authors.affiliation: Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel; mark.safro@weizmann.ac.il.
authors.forename: Mark G
authors.initials: MG
authors.lastname: Safro
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D000900:Anti-Bacterial Agents / Q000737:chemistry; D001665:Binding Sites; D003460:Crystallization; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000201:enzymology; D006860:Hydrogen Bonding; D006868:Hydrolysis; D008024:Ligands; D008958:Models, Molecular; D008968:Molecular Conformation; D010649:Phenylalanine / Q000737:chemistry; D010652:Phenylalanine-tRNA Ligase / Q000737:chemistry*; D055503:Protein Multimerization; D011500:Protein Synthesis Inhibitors / Q000737:chemistry; D011691:Puromycin / Q000737:chemistry*; D011789:Quantum Theory; D016963:Thermus thermophilus / Q000201:enzymology*; D014443:Tyrosine / Q000737:chemistry
chemical_list: D000596:Amino Acids; D000900:Anti-Bacterial Agents; D008024:Ligands; D011500:Protein Synthesis Inhibitors; D014443:Tyrosine; D010649:Phenylalanine; D011691:Puromycin; D010652:Phenylalanine-tRNA Ligase
keywords: aminoacyl-tRNA synthetases; biosynthesis; editing; puromycin; tRNA