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| | ==Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain== | | ==Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain== |
| - | <StructureSection load='1wk9' size='340' side='right' caption='[[1wk9]], [[Resolution|resolution]] 1.75Å' scene=''> | + | <StructureSection load='1wk9' size='340' side='right'caption='[[1wk9]], [[Resolution|resolution]] 1.75Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1wk9]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/"flavobacterium_thermophilum"_yoshida_and_oshima_1971 "flavobacterium thermophilum" yoshida and oshima 1971]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1WK9 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1WK9 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1wk9]] is a 1 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=1WK9 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WK9 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=TSB:5-O-(N-(L-THREONYL)-SULFAMOYL)ADENOSINE'>TSB</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.75Å</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1wka|1wka]]</td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=TSB:5-O-(N-(L-THREONYL)-SULFAMOYL)ADENOSINE'>TSB</scene></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'>[https://proteopedia.org/fgij/fg.htm?mol=1wk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wk9 OCA], [https://pdbe.org/1wk9 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wk9 RCSB], [https://www.ebi.ac.uk/pdbsum/1wk9 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wk9 ProSAT], [https://www.topsan.org/Proteins/RSGI/1wk9 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=1wk9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wk9 OCA], [http://pdbe.org/1wk9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1wk9 RCSB], [http://www.ebi.ac.uk/pdbsum/1wk9 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1wk9 ProSAT], [http://www.topsan.org/Proteins/RSGI/1wk9 TOPSAN]</span></td></tr> | + | |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://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] | + | [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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| | ==See Also== | | ==See Also== |
| - | *[[Aminoacyl tRNA Synthetase|Aminoacyl tRNA Synthetase]] | + | *[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Flavobacterium thermophilum yoshida and oshima 1971]] | + | [[Category: Large Structures]] |
| - | [[Category: Valine--tRNA ligase]] | + | [[Category: Thermus thermophilus]] |
| - | [[Category: Fukunaga, R]] | + | [[Category: Fukunaga R]] |
| - | [[Category: Structural genomic]]
| + | [[Category: Yokoyama S]] |
| - | [[Category: Yokoyama, S]] | + | |
| - | [[Category: Amino acid]]
| + | |
| - | [[Category: Cp1]]
| + | |
| - | [[Category: Editing]]
| + | |
| - | [[Category: Fidelity]]
| + | |
| - | [[Category: Ligase]]
| + | |
| - | [[Category: Rsgi]]
| + | |
| - | [[Category: Thermus thrmophilus]]
| + | |
| - | [[Category: Thr-am]]
| + | |
| - | [[Category: Translation]]
| + | |
| - | [[Category: 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 PubMed
The editing domain of valyl-tRNA synthetase (ValRS) is known to deacylate, or edit, misformed Thr-tRNA(Val) (post-transfer editing). Here, we determined the 1.7-Angstroms resolution crystal structure of the Thermus thermophilus ValRS editing domain. A comparison of the structure with the previously reported tRNA complex structure revealed conformational changes of the editing domain upon accommodation of the terminal A76; the "GTG loop" moves to expand the pocket, and the side chain of Phe-264 on the GTG loop rotates to interact with the A76 adenine ring. If these conformational changes did not occur, then C75 and A76 of the tRNA would clash with Phe-264. To elucidate the mechanism of the threonine side-chain recognition, we determined the crystal structure of the editing domain bound with [N-(L-threonyl)-sulfamoyl]adenosine at 1.7-Angstroms resolution. The gamma-OH of the threonyl moiety is recognized by the Lys-270, Thr-272, and Asp-279 side chains, which may reject the cognate valyl moiety. Accordingly, ValRS mutants with an Ala substitution for Lys-270 or Asp-279 synthesized significant amounts of Thr-tRNA(Val). The misproduced Thr-tRNA(Val) was hydrolyzed efficiently by the wild-type ValRS, but this post-transfer editing activity was drastically impaired by the Ala substitutions for Lys-270 and Asp-279 and was also decreased by those for Arg-216, Phe-264, and Thr-272. These results indicate that the threonyl moiety and A76 of Thr-tRNA(Val) are recognized by the Lys-270, Thr-272, and Asp-279 side chains and by the Phe-264 side chain, respectively, of the ValRS editing domain.
Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain.,Fukunaga R, Yokoyama S J Biol Chem. 2005 Aug 19;280(33):29937-45. Epub 2005 Jun 21. PMID:15970591[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Fukunaga R, Yokoyama S. Structural basis for non-cognate amino acid discrimination by the valyl-tRNA synthetase editing domain. J Biol Chem. 2005 Aug 19;280(33):29937-45. Epub 2005 Jun 21. PMID:15970591 doi:http://dx.doi.org/10.1074/jbc.M502668200
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