1iyw
From Proteopedia
(New page: 200px<br /><applet load="1iyw" size="450" color="white" frame="true" align="right" spinBox="true" caption="1iyw, resolution 4.0Å" /> '''Preliminary Structure...) |
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| - | [[Image:1iyw.jpg|left|200px]]<br /><applet load="1iyw" size=" | + | [[Image:1iyw.jpg|left|200px]]<br /><applet load="1iyw" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1iyw, resolution 4.0Å" /> | caption="1iyw, resolution 4.0Å" /> | ||
'''Preliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA Synthetase'''<br /> | '''Preliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA Synthetase'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The molecular interactions between valyl-tRNA synthetase (ValRS) and | + | 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== | ==About this Structure== | ||
| - | 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:// | + | 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]. |
==Reference== | ==Reference== | ||
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[[Category: Fukai, S.]] | [[Category: Fukai, S.]] | ||
[[Category: Nureki, O.]] | [[Category: Nureki, O.]] | ||
| - | [[Category: RSGI, RIKEN | + | [[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]] |
[[Category: Sekine, S.]] | [[Category: Sekine, S.]] | ||
[[Category: Shimada, A.]] | [[Category: Shimada, A.]] | ||
| - | [[Category: Vassylyev, D | + | [[Category: Vassylyev, D G.]] |
[[Category: Yokoyama, S.]] | [[Category: Yokoyama, S.]] | ||
[[Category: coiled coil]] | [[Category: coiled coil]] | ||
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[[Category: structural genomics]] | [[Category: structural genomics]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:17:19 2008'' |
Revision as of 11:17, 21 February 2008
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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. Active as Valine--tRNA ligase, with EC number 6.1.1.9 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 Thu Feb 21 13:17:19 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 genomics
