1IVS

CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE

Summary for 1IVS

• Entry DOI: 10.2210/pdb1ivs/pdb
• Descriptor: tRNA (Val), Valyl-tRNA synthetase, N-[VALINYL]-N'-[ADENOSYL]-DIAMINOSUFONE, ... (4 entities in total)
• Functional Keywords: rossmann fold, helix bundle, coiled coil, beta barrel, riken structural genomics/proteomics initiative, rsgi, structural genomics, ligase-rna complex, ligase/rna
• Biological source: Thermus thermophilus
• Cellular location: Cytoplasm: P96142
• Total number of polymer chains: 4
• Total formula weight: 247066.73

Authors

Fukai, S.,Nureki, O.,Sekine, S.-I.,Shimada, A.,Vassylyev, D.G.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2002-03-29, release date: 2003-02-11, Last modification date: 2023-12-27)

Primary citation

Fukai, S.,Nureki, O.,Sekine, S.-I.,Shimada, A.,Vassylyev, D.G.,Yokoyama, S.
Mechanism of molecular interactions for tRNA(Val) recognition by valyl-tRNA synthetase
RNA, 9:100-111, 2003

PubMed 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.

PubMed: 12554880
DOI: 10.1261/rna.2760703

Experimental method

X-RAY DIFFRACTION (2.9 Å)