Mechanism of molecular interactions for tRNA^Val recognition by valyl-tRNA synthetase

The molecular interactions between valyl-tRNA synthetase (ValRS) and tRNA^Val, with the C34-A35-C36 anticodon, from Thermus thermophilus were studied by crystallographic analysis and structure-based mutagenesis. In the ValRS-bound structure of tRNA^Val, the successive A35-C36 residues (the major identity elements) of tRNA^Val 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 tRNA^Val 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 K_M value for tRNA^Val 28-fold and decreased the k_cat value 19-fold in the aminoacylation. The tRNA^Val K_M and k_cat 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.