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

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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 tRNAValKM 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.