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1iyw
From Proteopedia
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|SITE= | |SITE= | ||
|LIGAND= | |LIGAND= | ||
| - | |ACTIVITY= [http://en.wikipedia.org/wiki/Valine--tRNA_ligase Valine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.9 6.1.1.9] | + | |ACTIVITY= <span class='plainlinks'>[http://en.wikipedia.org/wiki/Valine--tRNA_ligase Valine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.9 6.1.1.9] </span> |
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1gax|1GAX]], [[1ivs|1IVS]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1iyw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iyw OCA], [http://www.ebi.ac.uk/pdbsum/1iyw PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1iyw RCSB]</span> | ||
}} | }} | ||
| Line 36: | Line 39: | ||
[[Category: structural genomic]] | [[Category: structural genomic]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:26:39 2008'' |
Revision as of 18:26, 30 March 2008
| |||||||
| , resolution 4.0Å | |||||||
|---|---|---|---|---|---|---|---|
| Activity: | Valine--tRNA ligase, with EC number 6.1.1.9 | ||||||
| Related: | 1GAX, 1IVS
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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 Sun Mar 30 21:26:39 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
