1iyw

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Preliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA Synthetase

Overview

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 alpha-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.

About this Structure

1IYW 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

Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase., Fukai S, Nureki O, Sekine S, Shimada A, Vassylyev DG, Yokoyama S, RNA. 2003 Jan;9(1):100-11. PMID:12554880

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