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1udz

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[[Image:1udz.jpg|left|200px]]<br /><applet load="1udz" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="1udz, resolution 1.80&Aring;" />
 
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'''Isoleucyl-tRNA synthetase editing domain'''<br />
 
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==Overview==
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==Isoleucyl-tRNA synthetase editing domain==
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Isoleucyl-tRNA synthetase (IleRS) links tRNA(Ile) with not only its cognate isoleucine but also the nearly cognate valine. The CP1 domain of IleRS deacylates, or edits, the mischarged Val-tRNA(Ile). We determined the crystal structures of the Thermus thermophilus IleRS CP1 domain alone, and in its complex with valine at 1.8- and 2.0-A resolutions, respectively. In the complex structure, the Asp(328) residue, which was shown to be critical for the editing reaction against Val-tRNA(Ile) by a previous mutational analysis, recognizes the valine NH(3)(+) group. The valine side chain binding pocket is only large enough to accommodate valine, and the placement of an isoleucine model in this location revealed that the additional methylene group of isoleucine would clash with His(319). The H319A mutant of Escherichia coli IleRS reportedly deacylates the cognate Ile-tRNA(Ile) in addition to Val-tRNA(Ile), indicating that the valine-binding mode found in this study represents that in the Val-tRNA(Ile) editing reaction. Analyses of the Val-tRNA(Ile) editing activities of T. thermophilus IleRS mutants revealed the importance of Thr(228), Thr(229), Thr(230), and Asp(328), which are coordinated with water molecules in the present structure. The structural model for the Val-adenosine moiety of Val-tRNA(Ile) bound in the IleRS editing site revealed some interesting differences in the substrate binding and recognizing mechanisms between IleRS and T. thermophilus leucyl-tRNA synthetase. For example, the carbonyl oxygens of the amino acids are located opposite to each other, relative to the adenosine ribose ring, and are differently recognized.
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<StructureSection load='1udz' size='340' side='right'caption='[[1udz]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1udz]] 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=1UDZ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UDZ 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]] 1.8&#8491;</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=1udz FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1udz OCA], [https://pdbe.org/1udz PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1udz RCSB], [https://www.ebi.ac.uk/pdbsum/1udz PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1udz ProSAT], [https://www.topsan.org/Proteins/RSGI/1udz 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/ud/1udz_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=1udz 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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1UDZ is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thermus_thermophilus Thermus thermophilus]. 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1UDZ 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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Crystal structures of the CP1 domain from Thermus thermophilus isoleucyl-tRNA synthetase and its complex with L-valine., Fukunaga R, Fukai S, Ishitani R, Nureki O, Yokoyama S, J Biol Chem. 2004 Feb 27;279(9):8396-402. Epub 2003 Dec 12. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14672940 14672940]
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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: Fukai, S.]]
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[[Category: Fukai S]]
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[[Category: Fukunaga, R.]]
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[[Category: Fukunaga R]]
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[[Category: Ishitani, R.]]
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[[Category: Ishitani R]]
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[[Category: Nureki, O.]]
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[[Category: Nureki O]]
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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: aminoacyl-trna synthetase]]
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[[Category: cp1]]
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[[Category: editing]]
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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://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:23:33 2008''
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Current revision

Isoleucyl-tRNA synthetase editing domain

PDB ID 1udz

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