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

Dmitry Tworowski, Liron Klipcan, Moshe Peretz, Nina Moor, Mark G. Safro

Research output: Contribution to journalArticlepeer-review

8 Scopus citations

Abstract

At the amino acid binding and recognition step, phenylalanylt-RNA synthetase (PheRS) faces the challenge of discrimination between cognate phenylalanine and closely similar noncognate tyrosine. Resampling of Tyr-tRNAPhe 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 Tt PheRS. 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-tRNAPhe 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.

Original languageEnglish
Pages (from-to)3967-3972
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume112
Issue number13
DOIs
StatePublished - 31 Mar 2015
Externally publishedYes

Keywords

  • Aminoacyl-TRNA synthetases
  • Biosynthesis
  • Puromycin editing
  • TRNA

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