This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.
Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.
1ivs
From Proteopedia
| Line 4: | Line 4: | ||
|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'-[ADENOSYL]-DIAMINOSUFONE'>VAA</scene> | + | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=U:URIDINE-5'-MONOPHOSPHATE'>U</scene>, <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= <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= 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]) | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ivs FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ivs OCA], [http://www.ebi.ac.uk/pdbsum/1ivs PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ivs RCSB]</span> | ||
}} | }} | ||
| Line 30: | Line 33: | ||
[[Category: Vassylyev, D G.]] | [[Category: Vassylyev, D G.]] | ||
[[Category: Yokoyama, S.]] | [[Category: Yokoyama, S.]] | ||
| - | [[Category: VAA]] | ||
[[Category: beta barrel]] | [[Category: beta barrel]] | ||
[[Category: coiled coil]] | [[Category: coiled coil]] | ||
| Line 39: | Line 41: | ||
[[Category: structural genomic]] | [[Category: structural genomic]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:25:19 2008'' |
Revision as of 18:25, 30 March 2008
| |||||||
| , resolution 2.90Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Gene: | valS (Thermus thermophilus) | ||||||
| Activity: | Valine--tRNA ligase, with EC number 6.1.1.9 | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE
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
1IVS 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 21:25:19 2008
Categories: 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. | Beta barrel | Coiled coil | Helix bundle | Riken structural genomics/proteomics initiative | Rossmann fold | Rsgi | Structural genomic
