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National Academy of Sciences, Proceedings of the National Academy of Sciences, 10(100), p. 5676-5681, 2003

DOI: 10.1073/pnas.0631525100

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Expanding tRNA recognition of a tRNA synthetase by a single amino acid change

Journal article published in 2003 by Liang Feng, Debra Tumbula-Hansen, Helen Toogood ORCID, Dieter Soll
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

Aspartyl-tRNA synthetase (AspRS) occurs in two types: the discriminating enzyme (D-AspRS) forms only Asp-tRNA Asp , whereas the nondiscriminating enzyme (ND-AspRS) also synthesizes Asp-tRNA Asn , which is a required intermediate for protein synthesis in many organisms. We attempted to expand the tRNA recognition of the discriminating Thermococcus kodakaraensis AspRS to that of a ND-AspRS by in vitro mutagenesis. An alignment of 26 archaeal AspRS proteins revealed two positions (26 and 85 in the T. kodakaraensis sequence) whose amino acid identity changes according to the enzymes' tRNA specificity. In their anticodon-binding domain, D-AspRS proteins contain W26 (or Q26) and K85, compared with H26 and P85 in the ND-AspRSs. T. kodakaraensis AspRS gained the ability to form Asp-tRNA Asn in vitro when the W26H or K85P changes were introduced independently or in combination. In the aminoacylation of tRNA Asn or tRNA Asp transcripts, the mutant enzymes displayed at least a 100- to 500-fold change in tRNA specificity, as judged by the ratio of the k cat / K m values of Asp-tRNA Asp vs. Asp-tRNA Asn formation. That T. kodakaraensis mutant AspRSs mischarge tRNA Asn was also manifested in the higher level (1.7%) of aspartylation of unfractionated Pyrococcus tRNA compared with that achieved by the wild-type enzyme (0.9%). Northern blot analysis of the Asp-tRNA separated by acid/urea gel electrophoresis confirmed the in vitro synthesis of Asp-tRNA Asn . A structure-based model points to a direct interaction of K85 in T. kodakaraensis AspRS with the anticodon nucleotide C36 of tRNA Asp . Thus, a switch between D-AspRS and ND-AspRS enzymes could have evolved with only limited amino acid changes.