Kinetic Origin of Substrate Specificity in Post-Transfer Editing by Leucyl-tRNA Synthetase

• Published in: Journal of molecular biology 2018-01, Vol.430 (1), p.1-16
• Main Authors: Dulic, Morana, Cvetesic, Nevena, Zivkovic, Igor, Palencia, Andrés, Cusack, Stephen, Bertosa, Branimir, Gruic-Sovulj, Ita
• Format: Article
• Language: English
• Subjects: Acylation - genetics; Amino Acids - genetics; Amino Acyl-tRNA Synthetases - genetics; aminoacyl-tRNA synthetases; Aminoacylation - genetics; Binding Sites - genetics; catalytic RNA; Escherichia coli - genetics; Hydrolysis; Kinetics; Leucine-tRNA Ligase - genetics; norvaline; proofreading; RNA, Transfer, Amino Acyl - genetics; Substrate Specificity - genetics; substrate-assisted catalysis
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/j.jmb.2017.10.024

The intrinsic editing capacities of aminoacyl-tRNA synthetases ensure a high-fidelity translation of the amino acids that possess effective non-cognate aminoacylation surrogates. The dominant error-correction pathway comprises deacylation of misaminoacylated tRNA within the aminoacyl-tRNA synthetase editing site. To assess the origin of specificity of Escherichia coli leucyl-tRNA synthetase (LeuRS) against the cognate aminoacylation product in editing, we followed binding and catalysis independently using cognate leucyl- and non-cognate norvalyl-tRNALeu and their non-hydrolyzable analogues. We found that the amino acid part (leucine versus norvaline) of (mis)aminoacyl-tRNAs can contribute approximately 10-fold to ground-state discrimination at the editing site. In sharp contrast, the rate of deacylation of leucyl- and norvalyl-tRNALeu differed by about 104-fold. We further established the critical role for the A76 3′-OH group of the tRNALeu in post-transfer editing, which supports the substrate-assisted deacylation mechanism. Interestingly, the abrogation of the LeuRS specificity determinant threonine 252 did not improve the affinity of the editing site for the cognate leucine as expected, but instead substantially enhanced the rate of leucyl-tRNALeu hydrolysis. In line with that, molecular dynamics simulations revealed that the wild-type enzyme, but not the T252A mutant, enforced leucine to adopt the side-chain conformation that promotes the steric exclusion of a putative catalytic water. Our data demonstrated that the LeuRS editing site exhibits amino acid specificity of kinetic origin, arguing against the anticipated prominent role of steric exclusion in the rejection of leucine. This feature distinguishes editing from the synthetic site, which relies on ground-state discrimination in amino acid selection. [Display omitted] •The origin of specificity of the LeuRS editing domain was until now unresolved.•Ground-state binding does not contribute significantly to amino acid selection in editing.•Kinetic checkpoint operates to exclude Leu-tRNALeu from hydrolysis.•tRNA's A76 3′-OH group has a crucial role in post-transfer editing.•Opposing mechanisms govern substrate selectivity in the synthetic and editing site.