1ivs: Difference between revisions
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|PDB= 1ivs |SIZE=350|CAPTION= <scene name='initialview01'>1ivs</scene>, resolution 2.90Å | |PDB= 1ivs |SIZE=350|CAPTION= <scene name='initialview01'>1ivs</scene>, resolution 2.90Å | ||
|SITE= | |SITE= | ||
|LIGAND= <scene name='pdbligand=VAA:N-[VALINYL]-N | |LIGAND= <scene name='pdbligand=VAA:N-[VALINYL]-N'-[ADENOSYL]-DIAMINOSUFONE'>VAA</scene> | ||
|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= [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= valS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus]) | |GENE= valS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus]) | ||
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[[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 23 12:16:04 2008'' | ||
Revision as of 13:16, 23 March 2008
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| , resolution 2.90Å | |||||||
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| Ligands: | |||||||
| Gene: | valS (Thermus thermophilus) | ||||||
| Activity: | Valine--tRNA ligase, with EC number 6.1.1.9 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE
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
1IVS 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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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)
OCA- Pages with broken file links
- Single protein
- Thermus thermophilus
- Valine--tRNA ligase
- Fukai, S.
- Nureki, O.
- RSGI, RIKEN Structural Genomics/Proteomics Initiative.
- Sekine, S I.
- Shimada, A.
- Vassylyev, D G.
- Yokoyama, S.
- VAA
- Beta barrel
- Coiled coil
- Helix bundle
- Riken structural genomics/proteomics initiative
- Rossmann fold
- Rsgi
- Structural genomic