Aminoacyl-tRNA Substrate
and Enzyme Backbone Atoms
Contribute to Translational Quality Control by YbaK
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Abstract
Amino acids are covalently attached to their corresponding
transfer
RNAs (tRNAs) by aminoacyl-tRNA synthetases. Proofreading mechanisms
exist to ensure that high fidelity is maintained in this key step
in protein synthesis. Prolyl-tRNA synthetase (ProRS) can misacylate
cognate tRNA<sup>Pro</sup> with Ala and Cys. The <i>cis</i>-editing domain of ProRS (INS) hydrolyzes Ala-tRNA<sup>Pro</sup>,
whereas Cys-tRNA<sup>Pro</sup> is hydrolyzed by a single domain editing
protein, YbaK, <i>in trans</i>. Previous studies have proposed
a model of substrate-binding by bacterial YbaK and elucidated a substrate-assisted
mechanism of catalysis. However, the microscopic steps in this mechanism
have not been investigated. In this work, we carried out biochemical
experiments together with a detailed hybrid quantum mechanics/molecular
mechanics study to investigate the mechanism of catalysis by Escherichia coli YbaK. The results support a mechanism
wherein cyclization of the substrate Cys results in cleavage of the
Cys-tRNA ester bond. Protein side chains do not play a significant
role in YbaK catalysis. Instead, protein backbone atoms play crucial
roles in stabilizing the transition state, while the product is stabilized
by the 2′-OH of the tRNA