3pd4: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

OCA

@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:3pd4.jpg|left|200px]]
-<!--
+==Crystal structure of the editing domain of threonyl-tRNA synthetase from Pyrococcus abyssi in complex with glycyl-3'-aminoadenosine==
-The line below this paragraph, containing "STRUCTURE_3pd4", creates the "Structure Box" on the page.
+<StructureSection load='3pd4' size='340' side='right'caption='[[3pd4]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3pd4]] 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=3PD4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3PD4 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A3G:3-DEOXY-3-(GLYCYLAMINO)ADENOSINE'>A3G</scene></td></tr>
-{{STRUCTURE_3pd4|  PDB=3pd4  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3pd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3pd4 OCA], [https://pdbe.org/3pd4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3pd4 RCSB], [https://www.ebi.ac.uk/pdbsum/3pd4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3pd4 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 glycyl-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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3pd4" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_21098258}}, adds the Publication Abstract to the page
+*[[Aminoacyl tRNA synthetase 3D structures|Aminoacyl tRNA synthetase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 21098258 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_21098258}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-PD4 is a 2 chains structure with sequences 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=3PD4 OCA].
-==Reference==
-<ref group="xtra">PMID:21098258</ref><references group="xtra"/>
 [[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]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec  8 11:54:28 2010''