1iyw: Difference between revisions
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'''Preliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA Synthetase''' | {{Structure | ||
|PDB= 1iyw |SIZE=350|CAPTION= <scene name='initialview01'>1iyw</scene>, resolution 4.0Å | |||
|SITE= | |||
|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] | |||
|GENE= | |||
}} | |||
'''Preliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA Synthetase''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
1IYW is a [ | 1IYW is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IYW OCA]. | ||
==Reference== | ==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:[http:// | 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:[http://www.ncbi.nlm.nih.gov/pubmed/12554880 12554880] | ||
[[Category: Single protein]] | [[Category: Single protein]] | ||
[[Category: Thermus thermophilus]] | [[Category: Thermus thermophilus]] | ||
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[[Category: rossmann fold]] | [[Category: rossmann fold]] | ||
[[Category: rsgi]] | [[Category: rsgi]] | ||
[[Category: structural | [[Category: structural genomic]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 11:56:46 2008'' | ||
Revision as of 12:56, 20 March 2008
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| , resolution 4.0Å | |||||||
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| Activity: | Valine--tRNA ligase, with EC number 6.1.1.9 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Preliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA Synthetase
OverviewOverview
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 StructureAbout this Structure
1IYW is a Single protein structure of sequence from Thermus thermophilus. Full crystallographic information is available from OCA.
ReferenceReference
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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