1wnz

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(New page: 200px<br /><applet load="1wnz" size="450" color="white" frame="true" align="right" spinBox="true" caption="1wnz, resolution 1.70&Aring;" /> '''Isoleucyl-tRNA synth...)
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[[Image:1wnz.gif|left|200px]]<br /><applet load="1wnz" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1wnz, resolution 1.70&Aring;" />
 
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'''Isoleucyl-tRNA synthetase editing domain complexed with the post-transfer editing substrate analogue, Val-2AA'''<br />
 
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==Overview==
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==Isoleucyl-tRNA synthetase editing domain complexed with the post-transfer editing substrate analogue, Val-2AA==
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In isoleucyl-tRNA synthetase (IleRS), the "editing" domain contributes to, accurate aminoacylation by hydrolyzing the mis-synthesized intermediate, valyl-adenylate, in the "pre-transfer" editing mode and the incorrect, final product, valyl-tRNA(Ile), in the "post-transfer" editing mode. In, the present study, we determined the crystal structures of the Thermus, thermophilus IleRS editing domain complexed with the substrate analogues, in the pre and post-transfer modes, both at 1.7 A resolution. The active, site accommodates the two analogues differently, with the valine, side-chain rotated by about 120 degrees and the adenosine moiety oriented, upside down. The substrate-binding pocket adjusts to the, adenosine-monophosphate and adenosine moieties in the pre and, post-transfer modes, respectively, by flipping the Trp227 side-chain by, about 180 degrees . The substrate recognition mechanisms of IleRS are, characterized by the active-site rearrangement between the two editing, modes, and therefore differ from those of the homologous valyl and, leucyl-tRNA synthetases from T.thermophilus, in which the post-transfer, mode is predominant. Both modes of editing activities were reduced by, replacements of Trp227 with Ala, Val, Leu, and His, but not by those with, Phe and Tyr, indicating that the aromatic ring of Trp227 is important for, the substrate recognition. In both editing modes, Thr233 and His319, recognize the substrate valine side-chain, regardless of the valine, side-chain rotation, and reject the isoleucine side-chain. The T233A and, H319A mutants have detectable editing activities against the cognate, isoleucine.
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<StructureSection load='1wnz' size='340' side='right'caption='[[1wnz]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1wnz]] 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=1WNZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1WNZ FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.7&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=2VA:2-(L-VALYL)AMINO-2-DEOXYADENOSINE'>2VA</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1wnz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1wnz OCA], [https://pdbe.org/1wnz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1wnz RCSB], [https://www.ebi.ac.uk/pdbsum/1wnz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1wnz ProSAT], [https://www.topsan.org/Proteins/RSGI/1wnz TOPSAN]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/SYI_THET8 SYI_THET8] Catalyzes the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pretransfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'posttransfer' editing and involves deacylation of mischarged Val-tRNA(Ile) (By similarity).[HAMAP-Rule:MF_02003]
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/wn/1wnz_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1wnz ConSurf].
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<div style="clear:both"></div>
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==About this Structure==
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==See Also==
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1WNZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus] with 2VA as [http://en.wikipedia.org/wiki/ligand ligand]. Active as [http://en.wikipedia.org/wiki/Isoleucine--tRNA_ligase Isoleucine--tRNA ligase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=6.1.1.5 6.1.1.5] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1WNZ OCA].
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*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
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__TOC__
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==Reference==
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</StructureSection>
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Structural basis for substrate recognition by the editing domain of isoleucyl-tRNA synthetase., Fukunaga R, Yokoyama S, J Mol Biol. 2006 Jun 16;359(4):901-12. Epub 2006 Apr 25. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16697013 16697013]
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[[Category: Large Structures]]
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[[Category: Isoleucine--tRNA ligase]]
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[[Category: Single protein]]
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[[Category: Thermus thermophilus]]
[[Category: Thermus thermophilus]]
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[[Category: Fukunaga, R.]]
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[[Category: Fukunaga R]]
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[[Category: RSGI, RIKEN.Structural.Genomics/Proteomics.Initiative.]]
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[[Category: Yokoyama S]]
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[[Category: Yokoyama, S.]]
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[[Category: 2VA]]
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[[Category: ligase]]
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[[Category: national project on protein structural and functional analyses]]
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[[Category: nppsfa]]
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[[Category: riken structural genomics/proteomics initiative]]
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[[Category: rsgi]]
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[[Category: structural genomics]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Wed Nov 21 05:33:23 2007''
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Current revision

Isoleucyl-tRNA synthetase editing domain complexed with the post-transfer editing substrate analogue, Val-2AA

PDB ID 1wnz

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