Structural Basis for Discrimination of L-Phenylalanine from L-Tyrosine by Phenylalanyl-tRNA Synthetase

Department of Structural Biology, Weizmann Institute of Science, Rhovot, Central District, Israel
Structure (Impact Factor: 5.62). 01/2006; 13(12):1799-807. DOI: 10.1016/j.str.2005.08.013
Source: PubMed


Aminoacyl-tRNA synthetases (aaRSs) exert control over the faithful transfer of amino acids onto cognate tRNAs. Since chemical structures of various amino acids closely resemble each other, it is difficult to discriminate between them. Editing activity has been evolved by certain aaRSs to resolve the problem. In this study, we determined the crystal structures of complexes of T. thermophilus phenylalanyl-tRNA synthetase (PheRS) with L-tyrosine, p-chloro-phenylalanine, and a nonhydrolyzable tyrosyl-adenylate analog. The structures demonstrate plasticity of the synthetic site capable of binding substrates larger than phenylalanine and provide a structural basis for the proofreading mechanism. The editing site is localized at the B3/B4 interface, 35 A from the synthetic site. Glubeta334 plays a crucial role in the specific recognition of the Tyr moiety in the editing site. The tyrosyl-adenylate analog binds exclusively in the synthetic site. Both structural data and tyrosine-dependent ATP hydrolysis enhanced by tRNA(Phe) provide evidence for a preferential posttransfer editing pathway in the phenylalanine-specific system.

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Available from: Dmitry Tworowski, Oct 14, 2014
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    • "Errors during amino acid recognition do not usually compromise the accuracy of translation due to highly specific aaRS enzymes, and the widespread existence of editing mechanisms that proofread non-cognate amino acids. For example, phenylalanine tRNA synthetase (PheRS) edits mischarged Tyr-tRNA Phe at a hydrolytic editing site ∼30 Å from the synthetic active site (Roy et al., 2004; Kotik-Kogan et al., 2005). PheRS editing provides a key checkpoint in quality control, as mischarged Tyr-tRNA Phe is readily delivered to the ribosome by *For correspondence: ibba.1@ "
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    ABSTRACT: Aminoacyl-tRNA synthetases use a variety of mechanisms to ensure fidelity of the genetic code and ultimately select the correct amino acids to be used in protein synthesis. The physiological necessity of these quality control mechanisms in different environments remains unclear, as the cost vs benefit of accurate protein synthesis is difficult to predict. We show that in Escherichia coli, a non-coded amino acid produced through oxidative damage is a significant threat to the accuracy of protein synthesis and must be cleared by phenylalanine-tRNA synthetase in order to prevent cellular toxicity caused by mis-synthesized proteins. These findings demonstrate how stress can lead to the accumulation of non-canonical amino acids that must be excluded from the proteome in order to maintain cellular viability.
    Full-text · Article · Jun 2014 · eLife Sciences
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    • "For example, mischarging of tRNAAla with serine or glycine will result in erroneous propagation of the genomic message, and therefore needs to be ‘rectified’ by hydrolysis of the misacylated tRNAs such that another round of aminoacylation by, in this case, alanyl-tRNA synthetase results in Ala-tRNAAla18. Similarly, corrections by editing domain of phenylalanyl-tRNA synthetase (FRS) will protect mis-incorporation of tyrosines where phenylalanines are meant to be, by hydrolysis of mis-charged Tyr-tRNAPhe19. Importance of editing by aaRSs is also underscored by previous findings which show that mis-acylation can result in neurodegenerative diseases in mammals, growth defects in bacteria and in apoptosis82021. "
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    • "Crystallization and Structure Determination Crystallization of TtPheRS and HsmtPheRS with various ligands has been described in detail (Chernaya et al., 1987; Kotik-Kogan et al., 2005; Levin et al., 2007). Crystal soaking with L-dopa for TtPheRS and HsmtPheRS was carried out under conditions similar to those described. "
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