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J. Biol. Chem., Vol. 278, Issue 46, 45056-45061, November 14, 2003

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Structure-specific tRNA Determinants for Editing a Mischarged Amino Acid^*

Kirk Beebe, Eve Merriman, and Paul Schimmel

From the Department of Molecular Biology and Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037

Alanyl-tRNA synthetase efficiently aminoacylates tRNA^Ala and an RNA minihelix that comprises just one domain of the two-domain L-shaped tRNA structure. It also clears mischarged tRNA^Ala using a specialized domain in its C-terminal half. In contrast to full-length tRNA^Ala, minihelix^Ala was robustly mischarged and could not be edited. Addition in trans of the missing anticodon-containing domain did not activate editing of mischarged minihelix^Ala. To understand these differences between minihelix^Ala and tRNA^Ala, several chimeric full tRNAs were constructed. These had the acceptor stem of a non-cognate tRNA replaced with the stem of tRNA^Ala. The chimeric tRNAs collectively introduced multiple sequence changes in all parts but the acceptor stem. However, although the acceptor stem in isolation (as the minihelix) lacked determinants for editing, alanyl-tRNA synthetase effectively cleared a mischarged amino acid from each chimeric tRNA. Thus, a covalently continuous two-domain structure per se, not sequence, is a major determinant for clearance of errors of aminoacylation by alanyl-tRNA synthetase. Because errors of aminoacylation are known to be deleterious to cell growth, structure-specific determinants constitute a powerful selective pressure to retain the format of the two-domain L-shaped tRNA.

Received for publication, July 2, 2003 , and in revised form, August 20, 2003.

^* This work was supported by Grant GM15539 from the National Institutes of Health and by a fellowship from the National Foundation for Cancer Research. The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

Supported by National Institutes of Health postdoctoral fellowship.

To whom correspondence should be addressed: 10550 North Torrey Pines Rd., La Jolla, CA 92037. Tel.: 858-784-8970; Fax: 858-784-8990; E-mail: schimmel{at}scripps.edu.

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