1iyw

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[[Image:1iyw.jpg|left|200px]]<br /><applet load="1iyw" size="350" color="white" frame="true" align="right" spinBox="true"
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[[Image:1iyw.jpg|left|200px]]
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caption="1iyw, resolution 4.0&Aring;" />
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'''Preliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA Synthetase'''<br />
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{{Structure
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|PDB= 1iyw |SIZE=350|CAPTION= <scene name='initialview01'>1iyw</scene>, resolution 4.0&Aring;
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|SITE=
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|LIGAND=
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|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]
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|GENE=
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}}
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'''Preliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA Synthetase'''
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==Overview==
==Overview==
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==About this Structure==
==About this Structure==
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1IYW is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Active as [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] Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IYW OCA].
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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==
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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://ispc.weizmann.ac.il//pmbin/getpm?pmid=12554880 12554880]
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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]]
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[[Category: structural genomics]]
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[[Category: structural genomic]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:17:19 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 11:56:46 2008''

Revision as of 09:56, 20 March 2008

Image:1iyw.jpg


PDB ID 1iyw

Drag the structure with the mouse to rotate
, resolution 4.0Å
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


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

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