1iyw: Difference between revisions
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<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=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[1iyw]] is a 2 chain structure with sequence from [ | <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=' | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 4Å</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> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | |||
</table> | </table> | ||
== Function == | == 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 == | == Evolutionary Conservation == | ||
[[Image:Consurf_key_small.gif|200px|right]] | [[Image:Consurf_key_small.gif|200px|right]] | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | [[Category: Large Structures]] | ||
[[Category: | [[Category: Thermus thermophilus]] | ||
[[Category: Fukai | [[Category: Fukai S]] | ||
[[Category: Nureki | [[Category: Nureki O]] | ||
[[Category: Sekine S]] | |||
[[Category: Sekine | [[Category: Shimada A]] | ||
[[Category: Shimada | [[Category: Vassylyev DG]] | ||
[[Category: Vassylyev | [[Category: Yokoyama S]] | ||
[[Category: Yokoyama | |||
Latest revision as of 02:39, 28 December 2023
Preliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA SynthetasePreliminary Structure of Thermus thermophilus Ligand-Free Valyl-tRNA Synthetase
Structural highlights
FunctionSYV_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. See AlsoReferences |
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