3pd3: Difference between revisions

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-[[Image:3pd3.png|left|200px]]
-{{STRUCTURE_3pd3|  PDB=3pd3  |  SCENE=  }}
+==Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi in complex with threonyl-3'-aminoadenosine==
+<StructureSection load='3pd3' size='340' side='right'caption='[[3pd3]], [[Resolution|resolution]] 1.86&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3pd3]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PD3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PD3 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]] 1.86&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A3T:3-DEOXY-3-(L-THREONYLAMINO)ADENOSINE'>A3T</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=3pd3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pd3 OCA], [https://pdbe.org/3pd3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pd3 RCSB], [https://www.ebi.ac.uk/pdbsum/3pd3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pd3 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/SYT_PYRAB SYT_PYRAB]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Editing/proofreading by aminoacyl-tRNA synthetases is an important quality control step in the accurate translation of the genetic code that removes noncognate amino acids attached to tRNA. Defects in the process of editing result in disease conditions including neurodegeneration. While proofreading, the cognate amino acids larger by a methyl group are generally thought to be sterically rejected by the editing modules as envisaged by the "Double-Sieve Model." Strikingly using solution based direct binding studies, NMR-heteronuclear single quantum coherence (HSQC) and isothermal titration calorimetry experiments, with an editing domain of threonyl-tRNA synthetase, we show that the cognate substrate can gain access and bind to the editing pocket. High-resolution crystal structural analyses reveal that functional positioning of substrates rather than steric exclusion is the key for the mechanism of discrimination. A strategically positioned "catalytic water" molecule is excluded to avoid hydrolysis of the cognate substrate using a "RNA mediated substrate-assisted catalysis mechanism" at the editing site. The mechanistic proof of the critical role of RNA in proofreading activity is a completely unique solution to the problem of cognate-noncognate selection mechanism.
-===Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi in complex with threonyl-3'-aminoadenosine===
+Mechanistic insights into cognate substrate discrimination during proofreading in translation.,Hussain T, Kamarthapu V, Kruparani SP, Deshmukh MV, Sankaranarayanan R Proc Natl Acad Sci U S A. 2010 Nov 22. PMID:21098258<ref>PMID:21098258</ref>
-{{ABSTRACT_PUBMED_21098258}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3pd3" style="background-color:#fffaf0;"></div>
-[[3pd3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Pyrococcus_abyssi Pyrococcus abyssi]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3PD3 OCA].
 ==See Also==
-*[[Aminoacyl tRNA Synthetase|Aminoacyl tRNA Synthetase]]
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:021098258</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Pyrococcus abyssi]]
-[[Category: Threonine--tRNA ligase]]
+[[Category: Hussain T]]
-[[Category: Hussain, T.]]
+[[Category: Kamarthapu V]]
-[[Category: Kamarthapu, V.]]
+[[Category: Kruparani SP]]
-[[Category: Kruparani, S P.]]
+[[Category: Sankaranarayanan R]]
-[[Category: Sankaranarayanan, R.]]
-[[Category: Alpha/beta fold]]
-[[Category: Aminoacyl-trna synthetase]]
-[[Category: Deacylase]]
-[[Category: Editing]]
-[[Category: Ligase]]
-[[Category: Translation]]