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Distinct domains of tRNA synthetase recognize the same base pair


Synthesis of proteins containing errors (mistranslation) is prevented by aminoacyl transfer RNA synthetases through their accurate aminoacylation of cognate tRNAs and their ability to correct occasional errors of aminoacylation by editing reactions1,2,3,4,5. A principal source of mistranslation comes from mistaking glycine or serine for alanine, which can lead to serious cell and animal pathologies, including neurodegeneration3. A single specific G·U base pair (G3·U70) marks a tRNA for aminoacylation by alanyl-tRNA synthetase6,7,8,9. Mistranslation occurs when glycine or serine is joined to the G3·U70-containing tRNAs, and is prevented by the editing activity that clears the mischarged amino acid. Previously it was assumed that the specificity for recognition of tRNAAla for editing was provided by the same structural determinants as used for aminoacylation. Here we show that the editing site of alanyl-tRNA synthetase, as an artificial recombinant fragment, targets mischarged tRNAAla using a structural motif unrelated to that for aminoacylation so that, remarkably, two motifs (one for aminoacylation and one for editing) in the same enzyme independently can provide determinants for tRNAAla recognition. The structural motif for editing is also found naturally in genome-encoded protein fragments that are widely distributed in evolution10,11,12. These also recognize mischarged tRNAAla. Thus, through evolution, three different complexes with the same tRNA can guard against mistaking glycine or serine for alanine.

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Figure 1: Domains of AlaRS and AlaXp and deacylation activity of selected fragments.
Figure 2: AlaRS and its fragments are specific for tRNA Ala and influenced by the G3˙U70 base pair.
Figure 3: Multiple checkpoints of tRNA Ala recognition for prevention of mistranslation.

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We thank P. O’Maille for his gift of plasmid pH8GW and M. Sokabe for discussions about the model of the tRNA complex with Pyrococcus horikoshi AlaXp. This work was supported by grants from the National Institutes of Health, the Skaggs Foundation, and the National Foundation for Cancer Research.

Author Contributions K.B., M.M. and E.M. performed experiments and produced all materials. K.B., M.M. and P.S. conceived ideas, designed experiments, and wrote and edited the manuscript. All authors reviewed and approved the final manuscript.

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Correspondence to Paul Schimmel.

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Beebe, K., Mock, M., Merriman, E. et al. Distinct domains of tRNA synthetase recognize the same base pair. Nature 451, 90–93 (2008).

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