Solution to the double discrimination problem by the class II threonyl-tRNA synthetase

Abstract

Aminoacyl-tRNA synthetases play a crucial role in the translation of the genetic code by attaching amino acids to their cognate tRNAs through a two-step aminoacylation reaction. Threonyl-tRNA synthetase, a class II enzyme, faces a double discrimination problem against similar amino acids valine and s₁ erine. The structure of the enzyme in complex with its tRNA showed for the first time the presence of a zinc ion in the active site of an aminoacyl-tRNA synthetase. The zinc ion is directly involved in amino acid recognition by forming a pentacoordinate intermediate with threonine, thus making valine binding impossible. We showed recently using a cocrystal structure of the enzyme and a seryl-adenylate analog that serine could bind in the active site. However, the enzyme uses a separate and specific editing site in the N-terminal module for hydrolyzing the incorrectly formed ser-tRNA(Thr). Thus, both classes of synthetases use effectively the ability of the CCA-end of tRNA to switch between a hairpin and a helical conformation for aminoacylation and editing. The study shows that the RNA molecule is a key player in the evolution of this family of enzymes. Since the editing modules appeared much later compared to the catalytic domains, they could serve as new targets for drug design.