1iyw: Difference between revisions
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==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]] 4.00Å' scene=''> | <StructureSection load='1iyw' size='340' side='right' caption='[[1iyw]], [[Resolution|resolution]] 4.00Å' scene=''> | ||
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</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1gax|1gax]], [[1ivs|1ivs]]</td></tr> | </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1gax|1gax]], [[1ivs|1ivs]]</td></tr> | ||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr> | <tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><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></td></tr> | ||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1iyw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iyw OCA], [http://pdbe.org/1iyw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1iyw RCSB], [http://www.ebi.ac.uk/pdbsum/1iyw PDBsum], [http://www.topsan.org/Proteins/RSGI/1iyw TOPSAN]</span></td></tr> | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1iyw FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1iyw OCA], [http://pdbe.org/1iyw PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1iyw RCSB], [http://www.ebi.ac.uk/pdbsum/1iyw PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1iyw ProSAT], [http://www.topsan.org/Proteins/RSGI/1iyw TOPSAN]</span></td></tr> | ||
</table> | </table> | ||
== Function == | == Function == | ||
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Check<jmol> | Check<jmol> | ||
<jmolCheckbox> | <jmolCheckbox> | ||
<scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iy/1iyw_consurf.spt"</scriptWhenChecked> | <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> | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked> | ||
<text>to colour the structure by Evolutionary Conservation</text> | <text>to colour the structure by Evolutionary Conservation</text> | ||
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</div> | </div> | ||
<div class="pdbe-citations 1iyw" style="background-color:#fffaf0;"></div> | <div class="pdbe-citations 1iyw" style="background-color:#fffaf0;"></div> | ||
== References == | == References == | ||
<references/> | <references/> | ||
Revision as of 12:00, 17 January 2018
Preliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA SynthetasePreliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA Synthetase
Structural highlights
Function[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 Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf. Publication Abstract from PubMedThe 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. 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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