1v7o
From Proteopedia
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| - | [[Image:1v7o.jpg|left|200px]]<br /><applet load="1v7o" size="350" color="white" frame="true" align="right" spinBox="true" | ||
| - | caption="1v7o, resolution 2.62Å" /> | ||
| - | '''Alanyl-tRNA synthetase editing domain homologue protein from Pyrococcus horikoshii'''<br /> | ||
| - | == | + | ==Alanyl-tRNA synthetase editing domain homologue protein from Pyrococcus horikoshii== |
| + | <StructureSection load='1v7o' size='340' side='right'caption='[[1v7o]], [[Resolution|resolution]] 2.62Å' scene=''> | ||
| + | == Structural highlights == | ||
| + | <table><tr><td colspan='2'>[[1v7o]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_horikoshii_OT3 Pyrococcus horikoshii OT3]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1V7O OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V7O FirstGlance]. <br> | ||
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.62Å</td></tr> | ||
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MSE:SELENOMETHIONINE'>MSE</scene></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=1v7o FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v7o OCA], [https://pdbe.org/1v7o PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v7o RCSB], [https://www.ebi.ac.uk/pdbsum/1v7o PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v7o ProSAT]</span></td></tr> | ||
| + | </table> | ||
| + | == Function == | ||
| + | [https://www.uniprot.org/uniprot/ALAXS_PYRHO ALAXS_PYRHO] Functions in trans to edit the amino acid moiety from mischarged charged Ser-tRNA(Ala). Has little activity against Gly-tRNA(Ala). | ||
| + | == Evolutionary Conservation == | ||
| + | [[Image:Consurf_key_small.gif|200px|right]] | ||
| + | Check<jmol> | ||
| + | <jmolCheckbox> | ||
| + | <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/v7/1v7o_consurf.spt"</scriptWhenChecked> | ||
| + | <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked> | ||
| + | <text>to colour the structure by Evolutionary Conservation</text> | ||
| + | </jmolCheckbox> | ||
| + | </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=1v7o ConSurf]. | ||
| + | <div style="clear:both"></div> | ||
| + | <div style="background-color:#fffaf0;"> | ||
| + | == Publication Abstract from PubMed == | ||
AlaX is the homologue of the class II alanyl-tRNA synthetase editing domain and has been shown to exhibit autonomous editing activity against mischarged tRNA(Ala). Here, we present the structures of AlaX from the archaeon Pyrococcus horikoshii in apo form, complexed with zinc, and with noncognate amino acid l-serine and zinc. Together with mutational analysis, we demonstrated that the conserved Thr-30 hydroxyl group located near the beta-methylene of the bound serine is responsible for the discrimination of noncognate serine from cognate alanine, based on their chemical natures. Furthermore, we confirmed that the conserved Gln-584 in alanyl-tRNA synthetase, which corresponds to Thr-30 of AlaX, is also critical for discrimination. These observations strongly suggested conservation of the chemical discrimination among trans- and cis-editing of tRNA(Ala). | AlaX is the homologue of the class II alanyl-tRNA synthetase editing domain and has been shown to exhibit autonomous editing activity against mischarged tRNA(Ala). Here, we present the structures of AlaX from the archaeon Pyrococcus horikoshii in apo form, complexed with zinc, and with noncognate amino acid l-serine and zinc. Together with mutational analysis, we demonstrated that the conserved Thr-30 hydroxyl group located near the beta-methylene of the bound serine is responsible for the discrimination of noncognate serine from cognate alanine, based on their chemical natures. Furthermore, we confirmed that the conserved Gln-584 in alanyl-tRNA synthetase, which corresponds to Thr-30 of AlaX, is also critical for discrimination. These observations strongly suggested conservation of the chemical discrimination among trans- and cis-editing of tRNA(Ala). | ||
| - | + | Molecular basis of alanine discrimination in editing site.,Sokabe M, Okada A, Yao M, Nakashima T, Tanaka I Proc Natl Acad Sci U S A. 2005 Aug 16;102(33):11669-74. Epub 2005 Aug 8. PMID:16087889<ref>PMID:16087889</ref> | |
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| - | + | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |
| - | + | </div> | |
| - | + | <div class="pdbe-citations 1v7o" style="background-color:#fffaf0;"></div> | |
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| - | + | ==See Also== | |
| + | *[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Pyrococcus horikoshii OT3]] | ||
| + | [[Category: Okada A]] | ||
| + | [[Category: Sokabe M]] | ||
| + | [[Category: Tanaka I]] | ||
| + | [[Category: Yao M]] | ||
Current revision
Alanyl-tRNA synthetase editing domain homologue protein from Pyrococcus horikoshii
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