1ivs: Difference between revisions

Revision as of 20:28, 2 May 2008

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 Page seeded by OCA on Fri May 2 20:28:43 2008

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OCA

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 [[Image:1ivs.gif|left|200px]]
- {{Structure
+<!--
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+The line below this paragraph, containing "STRUCTURE_1ivs", creates the "Structure Box" on the page.
-|SITE=
+You may change the PDB parameter (which sets the PDB file loaded into the applet)
-|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>, <scene name='pdbligand=VAA:N-[VALINYL]-N&#39;-[ADENOSYL]-DIAMINOSUFONE'>VAA</scene>
+or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
-|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>
+or leave the SCENE parameter empty for the default display.
-|GENE= valS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])
+-->
-|DOMAIN=
+{{STRUCTURE_1ivs|  PDB=1ivs  |  SCENE=  }}
-|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>
-}}
 '''CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE'''
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 [[Category: Vassylyev, D G.]]
 [[Category: Yokoyama, S.]]
-[[Category: beta barrel]]
+[[Category: Beta barrel]]
-[[Category: coiled coil]]
+[[Category: Coiled coil]]
-[[Category: helix bundle]]
+[[Category: Helix bundle]]
-[[Category: riken structural genomics/proteomics initiative]]
+[[Category: Riken structural genomics/proteomics initiative]]
-[[Category: rossmann fold]]
+[[Category: Rossmann fold]]
-[[Category: rsgi]]
+[[Category: Rsgi]]
-[[Category: structural genomic]]
+[[Category: Structural genomic]]
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 20:28:43 2008''
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:25:19 2008''