1wka

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spinqualitylabelsall models 1wka, resolution 1.70Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain

Overview

The editing domain of valyl-tRNA synthetase (ValRS) is known to deacylate, or edit, misformed Thr-tRNA(Val) (post-transfer editing). Here, we, determined the 1.7-Angstroms resolution crystal structure of the Thermus, thermophilus ValRS editing domain. A comparison of the structure with the, previously reported tRNA complex structure revealed conformational changes, of the editing domain upon accommodation of the terminal A76; the "GTG, loop" moves to expand the pocket, and the side chain of Phe-264 on the GTG, loop rotates to interact with the A76 adenine ring. If these, conformational changes did not occur, then C75 and A76 of the tRNA would, clash with Phe-264. To elucidate the mechanism of the threonine side-chain, recognition, we determined the crystal structure of the editing domain, bound with [N-(L-threonyl)-sulfamoyl]adenosine at 1.7-Angstroms, resolution. The gamma-OH of the threonyl moiety is recognized by the, Lys-270, Thr-272, and Asp-279 side chains, which may reject the cognate, valyl moiety. Accordingly, ValRS mutants with an Ala substitution for, Lys-270 or Asp-279 synthesized significant amounts of Thr-tRNA(Val). The, misproduced Thr-tRNA(Val) was hydrolyzed efficiently by the wild-type, ValRS, but this post-transfer editing activity was drastically impaired by, the Ala substitutions for Lys-270 and Asp-279 and was also decreased by, those for Arg-216, Phe-264, and Thr-272. These results indicate that the, threonyl moiety and A76 of Thr-tRNA(Val) are recognized by the Lys-270, Thr-272, and Asp-279 side chains and by the Phe-264 side chain, respectively, of the ValRS editing domain.

About this Structure

1WKA is a Single protein structure of sequence from Thermus thermophilus. Active as Valine--tRNA ligase, with EC number 6.1.1.9 Full crystallographic information is available from OCA.

Reference

Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain., Fukunaga R, Yokoyama S, J Biol Chem. 2005 Aug 19;280(33):29937-45. Epub 2005 Jun 21. PMID:15970591

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