title: Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase.
abstract: 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.
authors.affiliation: Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Japan.
authors.forename: Shuya
authors.initials: S
authors.lastname: Fukai
authors.forename: Osamu
authors.initials: O
authors.lastname: Nureki
authors.forename: Shun-Ichi
authors.initials: S
authors.lastname: Sekine
authors.forename: Atsushi
authors.initials: A
authors.lastname: Shimada
authors.forename: Dmitry G
authors.initials: DG
authors.lastname: Vassylyev
authors.forename: Shigeyuki
authors.initials: S
authors.lastname: Yokoyama
mesh_terms: D000926:Anticodon; D006860:Hydrogen Bonding; D007700:Kinetics; D008958:Models, Molecular; D011487:Protein Conformation; D012366:RNA, Transfer, Val / Q000378:metabolism*; D016963:Thermus thermophilus / Q000201:enzymology; D014637:Valine-tRNA Ligase / Q000737:chemistry / Q000378:metabolism*
chemical_list: D000926:Anticodon; D012366:RNA, Transfer, Val; D014637:Valine-tRNA Ligase