Universal pathway for posttransfer editing reactions: insights from the crystal structure of TtPheRS with puromycin.

TitleUniversal pathway for posttransfer editing reactions: insights from the crystal structure of TtPheRS with puromycin.
Publication TypeJournal Article
Year of Publication2015
AuthorsTworowski, D, Klipcan, L, Peretz, M, Moor, N, Safro, MG
JournalProc Natl Acad Sci U S A
Volume112
Issue13
Pagination3967-72
Date Published2015 Mar 31
ISSN1091-6490
KeywordsAmino Acids, Anti-Bacterial Agents, Binding Sites, Crystallization, Crystallography, X-Ray, Escherichia coli, Hydrogen Bonding, Hydrolysis, Ligands, Models, Molecular, Molecular Conformation, Phenylalanine, Phenylalanine-tRNA Ligase, Protein Multimerization, Protein Synthesis Inhibitors, Puromycin, Quantum Theory, Thermus thermophilus, Tyrosine
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.

DOI10.1073/pnas.1414852112
Alternate JournalProc. Natl. Acad. Sci. U.S.A.
Citation Key10.1073/pnas.1414852112
PubMed ID25775602
PubMed Central IDPMC4386372