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[[Image:1iyw.jpg|left|200px]]
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{{STRUCTURE_1iyw|  PDB=1iyw  |  SCENE=  }}
'''Preliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA Synthetase'''


==Preliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA Synthetase==
<StructureSection load='1iyw' size='340' side='right'caption='[[1iyw]], [[Resolution|resolution]] 4.00&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1iyw]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IYW OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IYW FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 4&#8491;</td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1iyw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iyw OCA], [https://pdbe.org/1iyw PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1iyw RCSB], [https://www.ebi.ac.uk/pdbsum/1iyw PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1iyw ProSAT], [https://www.topsan.org/Proteins/RSGI/1iyw TOPSAN]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/SYV_THETH SYV_THETH] Catalyzes the attachment of valine to tRNA(Val). As ValRS can inadvertently accommodate and process structurally similar amino acids such as threonine, to avoid such errors, it has a "posttransfer" editing activity that hydrolyzes mischarged Thr-tRNA(Val) in a tRNA-dependent manner.[HAMAP-Rule:MF_02004]
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
  <jmolCheckbox>
    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iy/1iyw_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
    <text>to colour the structure by Evolutionary Conservation</text>
  </jmolCheckbox>
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1iyw ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.


==Overview==
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<ref>PMID:12554880</ref>
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==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
1IYW is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IYW OCA].
</div>
<div class="pdbe-citations 1iyw" style="background-color:#fffaf0;"></div>


==Reference==
==See Also==
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:[http://www.ncbi.nlm.nih.gov/pubmed/12554880 12554880]
*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
[[Category: Single protein]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
[[Category: Valine--tRNA ligase]]
[[Category: Fukai S]]
[[Category: Fukai, S.]]
[[Category: Nureki O]]
[[Category: Nureki, O.]]
[[Category: Sekine S]]
[[Category: RSGI, RIKEN Structural Genomics/Proteomics Initiative.]]
[[Category: Shimada A]]
[[Category: Sekine, S.]]
[[Category: Vassylyev DG]]
[[Category: Shimada, A.]]
[[Category: Yokoyama S]]
[[Category: Vassylyev, D G.]]
[[Category: Yokoyama, S.]]
[[Category: Coiled coil]]
[[Category: Riken structural genomics/proteomics initiative]]
[[Category: Rossmann fold]]
[[Category: Rsgi]]
[[Category: Structural genomic]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 20:36:03 2008''
Retrieved from "https://proteopedia.org/1iyw"