2qes: Difference between revisions

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-[[Image:2qes.jpg|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_2qes", creates the "Structure Box" on the page.
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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-{{STRUCTURE_2qes|  PDB=2qes  |  SCENE=  }}
-'''Crystal structure of the ribosome inactivating protein PDL4 from P. dioica leaves in complex with adenine'''
+==Crystal structure of the ribosome inactivating protein PDL4 from P. dioica leaves in complex with adenine==
+<StructureSection load='2qes' size='340' side='right'caption='[[2qes]], [[Resolution|resolution]] 1.24&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2qes]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Phytolacca_dioica Phytolacca dioica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QES OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2QES 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]] 1.24&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADE:ADENINE'>ADE</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=2qes FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2qes OCA], [https://pdbe.org/2qes PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2qes RCSB], [https://www.ebi.ac.uk/pdbsum/2qes PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2qes ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RIPL2_PHYDI RIPL2_PHYDI] Inhibits protein synthesis. Does not cleave supercoiled pBR322 dsDNA.<ref>PMID:10213004</ref> <ref>PMID:15899692</ref>
+== 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/qe/2qes_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=2qes ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The ribosome inactivating protein PD-L4 from Phytolacca dioica is a N-beta-glycosidase, probably involved in plant defence. The crystal structures of wild type PD-L4 and of the S211A PD-L4 mutant with significantly decreased catalytic activity were determined at atomic resolution. To determine the structural determinants for the reduced activity of S211A PD-L4, both forms have also been co-crystallized with adenine, the major product of PD-L4 catalytic reaction. In the structure of the S211A mutant, the cavity formed by the lack of the Ser hydroxyl group is filled by a water molecule; the insertion of this non-isosteric group leads to small albeit concerted changes in the tightly packed active site of the enzyme. These changes have been correlated to the different activity of the mutant enzyme. This work highlights the importance of atomic resolution studies for the deep understanding of enzymatic properties. Proteins 2008. (c) 2007 Wiley-Liss, Inc.
-==Overview==
+Atomic resolution (1.1 A) structure of the ribosome-inactivating protein PD-L4 from Phytolacca dioica L. leaves.,Ruggiero A, Chambery A, Maro AD, Parente A, Berisio R Proteins. 2007 Oct 26;71(1):8-15. PMID:17963235<ref>PMID:17963235</ref>
-The ribosome inactivating protein PD-L4 from Phytolacca dioica is a N-beta-glycosidase, probably involved in plant defence. The crystal structures of wild type PD-L4 and of the S211A PD-L4 mutant with significantly decreased catalytic activity were determined at atomic resolution. To determine the structural determinants for the reduced activity of S211A PD-L4, both forms have also been co-crystallized with adenine, the major product of PD-L4 catalytic reaction. In the structure of the S211A mutant, the cavity formed by the lack of the Ser hydroxyl group is filled by a water molecule; the insertion of this non-isosteric group leads to small albeit concerted changes in the tightly packed active site of the enzyme. These changes have been correlated to the different activity of the mutant enzyme. This work highlights the importance of atomic resolution studies for the deep understanding of enzymatic properties. Proteins 2008. (c) 2007 Wiley-Liss, Inc.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-QES is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Phytolacca_dioica Phytolacca dioica]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2QES OCA].
+</div>
+<div class="pdbe-citations 2qes" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-Atomic resolution (1.1 A) structure of the ribosome-inactivating protein PD-L4 from Phytolacca dioica L. leaves., Ruggiero A, Chambery A, Maro AD, Parente A, Berisio R, Proteins. 2007 Oct 26;71(1):8-15. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17963235 17963235]
+*[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Phytolacca dioica]]
-[[Category: Single protein]]
+[[Category: Berisio R]]
-[[Category: RRNA N-glycosylase]]
+[[Category: Ruggiero A]]
-[[Category: Berisio, R.]]
-[[Category: Ruggiero, A.]]
-[[Category: Crystal]]
-[[Category: Hydrolase]]
-[[Category: Ribosome inactivating protein]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May  4 14:49:51 2008''