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1ivs

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[[Image:1ivs.gif|left|200px]]
[[Image:1ivs.gif|left|200px]]
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{{Structure
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<!--
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|PDB= 1ivs |SIZE=350|CAPTION= <scene name='initialview01'>1ivs</scene>, resolution 2.90&Aring;
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The line below this paragraph, containing "STRUCTURE_1ivs", creates the "Structure Box" on the page.
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|SITE=
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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|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>
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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|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>
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or leave the SCENE parameter empty for the default display.
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|GENE= valS ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=274 Thermus thermophilus])
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|DOMAIN=
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{{STRUCTURE_1ivs| PDB=1ivs | SCENE= }}
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|RELATEDENTRY=
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|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>
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}}
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'''CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS VALYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(VAL) AND VALYL-ADENYLATE ANALOGUE'''
'''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: Vassylyev, D G.]]
[[Category: Yokoyama, S.]]
[[Category: Yokoyama, S.]]
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[[Category: beta barrel]]
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[[Category: Beta barrel]]
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[[Category: coiled coil]]
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[[Category: Coiled coil]]
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[[Category: helix bundle]]
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[[Category: Helix bundle]]
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[[Category: riken structural genomics/proteomics initiative]]
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[[Category: Riken structural genomics/proteomics initiative]]
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[[Category: rossmann fold]]
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[[Category: Rossmann fold]]
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[[Category: rsgi]]
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[[Category: Rsgi]]
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[[Category: structural genomic]]
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[[Category: Structural genomic]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 20:28:43 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:25:19 2008''
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Revision as of 17:28, 2 May 2008

Image:1ivs.gif

Template:STRUCTURE 1ivs

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 Fri May 2 20:28:43 2008

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