Mechanism of molecular interactions for tRNAVal recognition by valyl-tRNA synthetase

Shuya Fukai, Osamu Nureki, Shun Ichi Sekine, Atsushi Shimada, Dmitry G. Vassylyev, Shigeyuki Yokoyama

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49 Citations (Scopus)

Abstract

The molecular interactions between valyl-tRNA synthetase (ValRS) and tRNAVal, with the C34-A35-C36 anticodon, from Thermus thermophilus were studied by crystallographic analysis and structure-based mutagenesis. In the ValRS-bound structure of tRNAVal, the successive A35-C36 residues (the major identity elements) of tRNAVal are base-stacked upon each other, and fit into a pocket on the α-helix bundle domain of ValRS. Hydrogen bonds are formed between ValRS and A35-C36 of tRNAVal in a base-specific manner. The C-terminal coiled-coil domain of ValRS interacts electrostatically with A20 and hydrophobically with the G19-C56 tertiary base pair. The loss of these interactions by the deletion of the coiled-coil domain of ValRS increased the KM value for tRNAVal 28-fold and decreased the kcat value 19-fold in the aminoacylation. The tRNAVal KM and kcat values were increased 21-fold and decreased 32-fold, respectively, by the disruption of the G18-U55 and G19·C56 tertiary base pairs, which associate the D- and T-loops for the formation of the L-shaped tRNA structure. Therefore, the coiled-coil domain of ValRS is likely to stabilize the L-shaped tRNA structure during the aminoacylation reaction.

Original languageEnglish
Pages (from-to)100-111
Number of pages12
JournalRNA
Volume9
Issue number1
DOIs
Publication statusPublished - Jan 1 2003
Externally publishedYes

All Science Journal Classification (ASJC) codes

  • Molecular Biology

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  • Cite this

    Fukai, S., Nureki, O., Sekine, S. I., Shimada, A., Vassylyev, D. G., & Yokoyama, S. (2003). Mechanism of molecular interactions for tRNAVal recognition by valyl-tRNA synthetase. RNA, 9(1), 100-111. https://doi.org/10.1261/rna.2760703