ArticleThe journal of physical chemistry. B2013
Aminoacyl-tRNA substrate and enzyme backbone atoms contribute to translational quality control by YbaK.
Article in The journal of physical chemistry. B, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 16 citations in OpenAlex.
- Article
- The role of tRNA identity elements in aminoacyl-tRNA editing.Frontiers in microbiology · 2024Review
- The characterization ofMicrobial genomics · 2022Article
- The feather degradation mechanisms of a new Streptomyces sp. isolate SCUT-3.Communications biology · 2020Article
- Aminoacyl-tRNA Synthetases in the Bacterial World.EcoSal Plus · 2016Review
- Homologous trans-editing factors with broad tRNA specificity prevent mistranslation caused by serine/threonine misactivation.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Distinct tRNA recognition strategies used by a homologous family of editing domains prevent mistranslation.Nucleic acids research · 2014Article
- Strictly conserved lysine of prolyl-tRNA Synthetase editing domain facilitates binding and positioning of misacylated tRNA(Pro.).Biochemistry · 2014Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
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(Pro) with Ala and Cys. The cis-editing domain of ProRS (INS) hydrolyzes Ala-tRNA(Pro), whereas Cys-tRNA(Pro) is hydrolyzed by a single domain editing protein, YbaK, in trans. 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.
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