2qes: Difference between revisions

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-{{Seed}}
-[[Image:2qes.png|left|200px]]
-<!--
+==Crystal structure of the ribosome inactivating protein PDL4 from P. dioica leaves in complex with adenine==
-The line below this paragraph, containing "STRUCTURE_2qes", creates the "Structure Box" on the page.
+<StructureSection load='2qes' size='340' side='right'caption='[[2qes]], [[Resolution|resolution]] 1.24&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'>[[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>
-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]] 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>
-{{STRUCTURE_2qes|  PDB=2qes  |  SCENE=  }}
+<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.
-===Crystal structure of the ribosome inactivating protein PDL4 from P. dioica leaves in complex with adenine===
+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>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2qes" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_17963235}}, adds the Publication Abstract to the page
+*[[Ribosome inactivating protein 3D structures|Ribosome inactivating protein 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 17963235 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_17963235}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-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].
-==Reference==
-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]
 [[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 Jul 27 13:47:16 2008''