2vnx: Difference between revisions

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-[[Image:2vnx.png|left|200px]]
-{{STRUCTURE_2vnx|  PDB=2vnx  |  SCENE=  }}
+==Crystal structure of soybean ascorbate peroxidase mutant W41A after exposure to a high dose of x-rays==
+<StructureSection load='2vnx' size='340' side='right'caption='[[2vnx]], [[Resolution|resolution]] 1.50&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2vnx]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VNX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VNX 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]] 1.5&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=2vnx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vnx OCA], [https://pdbe.org/2vnx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vnx RCSB], [https://www.ebi.ac.uk/pdbsum/2vnx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vnx ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q43758_SOYBN Q43758_SOYBN]
+== 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/vn/2vnx_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=2vnx ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+We have previously shown [Badyal, S. K., et al. (2006) J. Biol. Chem. 281, 24512-24520] that the distal histidine (His42) in the W41A variant of ascorbate peroxidase binds to the heme iron in the ferric form of the protein but that binding of the substrate triggers a conformational change in which His42 dissociates from the heme. In this work, we show that this conformational rearrangement also occurs upon reduction of the heme iron. Thus, we present X-ray crystallographic data to show that reduction of the heme leads to dissociation of His42 from the iron in the ferrous form of W41A; spectroscopic and ligand binding data support this observation. Structural evidence indicates that heme reduction occurs through formation of a reduced, bis-histidine-ligated species that subsequently decays by dissociation of His42 from the heme. Collectively, the data provide clear evidence that conformational movement within the same heme active site can be controlled by both ligand binding and metal oxidation state. These observations are consistent with emerging data on other, more complex regulatory and sensing heme proteins, and the data are discussed in the context of our developing views in this area.
-===CRYSTAL STRUCTURE OF SOYBEAN ASCORBATE PEROXIDASE MUTANT W41A AFTER EXPOSURE TO A HIGH DOSE OF X-RAYS===
+Iron oxidation state modulates active site structure in a heme peroxidase(,).,Badyal SK, Metcalfe CL, Basran J, Efimov I, Moody PC, Raven EL Biochemistry. 2008 Apr 15;47(15):4403-9. Epub 2008 Mar 20. PMID:18351739<ref>PMID:18351739</ref>
-{{ABSTRACT_PUBMED_18351739}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2vnx" style="background-color:#fffaf0;"></div>
-[[2vnx]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Glycine_max Glycine max]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VNX OCA].
 ==See Also==
-*[[Ascorbate peroxidase|Ascorbate peroxidase]]
+*[[Ascorbate peroxidase 3D structures|Ascorbate peroxidase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:018351739</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Glycine max]]
-[[Category: Oxidoreductase]]
+[[Category: Large Structures]]
-[[Category: Badyal, S K.]]
+[[Category: Badyal SK]]
-[[Category: Metcalfe, C L.]]
+[[Category: Metcalfe CL]]
-[[Category: Moody, P C.E.]]
+[[Category: Moody PCE]]
-[[Category: Raven, E L.]]
+[[Category: Raven EL]]
-[[Category: Apx]]
-[[Category: Heme enzyme]]
-[[Category: Oxidoreductase]]
-[[Category: Peroxidase]]
-[[Category: Reduction by x-ray]]