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Structural modelling of the complex of leucyl-tRNA synthetase and mis-aminoacylated tRNA |
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| Authors: | Yohsuke Hagiwara Osamu Nureki Masaru Tateno |
| Affiliation: | a Center for Computational Sciences, University of Tsukuba, Division of Materials and Life Sciences, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8571, Japan b Graduate School of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba Science City, Ibaraki 305-8571, Japan c Institute of Medical Science, University of Tokyo, Shirokanedai 4-6-1, Minatoku, Tokyo 108-8639, Japan |
| Abstract: | To assure fidelity of translation, class Ia aminoacyl-tRNA synthetases (aaRSs) edit mis-aminoacylated tRNAs. Mis-attached amino acids and structural water molecules are not included simultaneously in the current crystal structures of the aaRS•tRNA complexes, where the 3′-ends (adenine 76; A76) are bound to the editing sites. A structural model of the completely solvated leucyl-tRNA synthetase complexed with valyl-tRNALeu was constructed by exploiting molecular dynamics simulations modified for the present modelling. The results showed that the ribose conformation of A76 is distinct from those observed in the above-mentioned crystal structures, which could be derived from structural constraints in a sandwiched manner induced by the mis-attached valine and tRNALeu. |
| Keywords: | aaRS, aminoacyl-tRNA synthetase LeuRS, leucyl-tRNA synthetase ValRS, valyl-tRNA synthetase MD, molecular dynamics CP1, connective polypeptide 1 |
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