1iyw
From Proteopedia
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'''Preliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA Synthetase''' | '''Preliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA Synthetase''' | ||
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[[Category: Vassylyev, D G.]] | [[Category: Vassylyev, D G.]] | ||
[[Category: Yokoyama, S.]] | [[Category: Yokoyama, S.]] | ||
| - | [[Category: | + | [[Category: Coiled coil]] |
| - | [[Category: | + | [[Category: Riken structural genomics/proteomics initiative]] |
| - | [[Category: | + | [[Category: Rossmann fold]] |
| - | [[Category: | + | [[Category: Rsgi]] |
| - | [[Category: | + | [[Category: Structural genomic]] |
| - | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 20:36:03 2008'' | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | |
Revision as of 17:36, 2 May 2008
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. 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 Page seeded by OCA on Fri May 2 20:36:03 2008
Categories: Single protein | Thermus thermophilus | Valine--tRNA ligase | Fukai, S. | Nureki, O. | RSGI, RIKEN Structural Genomics/Proteomics Initiative. | Sekine, S. | Shimada, A. | Vassylyev, D G. | Yokoyama, S. | Coiled coil | Riken structural genomics/proteomics initiative | Rossmann fold | Rsgi | Structural genomic
