Structural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetase

Atsushi Shimada, Osamu Nureki, Mie Goto, Seizo Takahashi, Shigeyuki Yokoyama

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39 Citations (Scopus)

Abstract

Arginyl-tRNA synthetase (ArgRS) recognizes two major identity elements of tRNAArg: A20, located at the outside corner of the L-shaped tRNA, and C35, the second letter of the anticodon. Only a few exceptional organisms, such as the yeast Saccharomyces cerevisiae, lack A20 in tRNAArg. In the present study, we solved the crystal structure of a typical A20-recognizing ArgRS from Thermus thermophilus at 2.3 Å resolution. The structure of the T. thermophilus ArgRS was found to be similar to that of the previously reported S. cerevisiae ArgRS, except for short insertions and a concomitant conformational change in the N-terminal domain. The structure of the yeast ArgRS-tRNAArg complex suggested that two residues in the unique N-terminal domain, Tyr77 and Asn79, which are phylogenetically invariant in the ArgRSs from all organisms with A20 in tRNAArgs, are involved in A20 recognition. However, in a docking model constructed based on the yeast ArgRS-tRNAArg and T. thermophilus ArgRS structures, Tyr77 and Asn79 are not close enough to make direct contact with A20, because of the conformational change in the N-terminal domain. Nevertheless, the replacement of Tyr77 or Asn79 by Ala severely reduced the arginylation efficiency. Therefore, some conformational change around A20 is necessary for the recognition. Surprisingly, the N79D mutant equally recognized A20 and G20, with only a slight reduction in the arginylation efficiency as compared with the wild-type enzyme. Other mutants of Asn79 also exhibited broader specificity for the nucleotide at position 20 of tRNAArg. We propose a model of A20 recognition by the ArgRS that is consistent with the present results of the mutational analyses.

Original languageEnglish
Pages (from-to)13537-13542
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Volume98
Issue number24
DOIs
Publication statusPublished - Nov 20 2001
Externally publishedYes

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Arginine-tRNA Ligase
RNA, Transfer, Arg
Thermus thermophilus
Yeasts
Saccharomyces cerevisiae
Anticodon
Transfer RNA
Nucleotides

All Science Journal Classification (ASJC) codes

  • General

Cite this

Structural and mutational studies of the recognition of the arginine tRNA-specific major identity element, A20, by arginyl-tRNA synthetase. / Shimada, Atsushi; Nureki, Osamu; Goto, Mie; Takahashi, Seizo; Yokoyama, Shigeyuki.

In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 98, No. 24, 20.11.2001, p. 13537-13542.

Research output: Contribution to journalArticle

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abstract = "Arginyl-tRNA synthetase (ArgRS) recognizes two major identity elements of tRNAArg: A20, located at the outside corner of the L-shaped tRNA, and C35, the second letter of the anticodon. Only a few exceptional organisms, such as the yeast Saccharomyces cerevisiae, lack A20 in tRNAArg. In the present study, we solved the crystal structure of a typical A20-recognizing ArgRS from Thermus thermophilus at 2.3 {\AA} resolution. The structure of the T. thermophilus ArgRS was found to be similar to that of the previously reported S. cerevisiae ArgRS, except for short insertions and a concomitant conformational change in the N-terminal domain. The structure of the yeast ArgRS-tRNAArg complex suggested that two residues in the unique N-terminal domain, Tyr77 and Asn79, which are phylogenetically invariant in the ArgRSs from all organisms with A20 in tRNAArgs, are involved in A20 recognition. However, in a docking model constructed based on the yeast ArgRS-tRNAArg and T. thermophilus ArgRS structures, Tyr77 and Asn79 are not close enough to make direct contact with A20, because of the conformational change in the N-terminal domain. Nevertheless, the replacement of Tyr77 or Asn79 by Ala severely reduced the arginylation efficiency. Therefore, some conformational change around A20 is necessary for the recognition. Surprisingly, the N79D mutant equally recognized A20 and G20, with only a slight reduction in the arginylation efficiency as compared with the wild-type enzyme. Other mutants of Asn79 also exhibited broader specificity for the nucleotide at position 20 of tRNAArg. We propose a model of A20 recognition by the ArgRS that is consistent with the present results of the mutational analyses.",
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