2wd4: Difference between revisions

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-{{STRUCTURE_2wd4|  PDB=2wd4  |  SCENE=  }}
-===ASCORBATE PEROXIDASE AS A HEME OXYGENASE: W41A VARIANT PRODUCT WITH T-BUTYL PEROXIDE===
-{{ABSTRACT_PUBMED_19309109}}
-==About this Structure==
+==Ascorbate Peroxidase as a heme oxygenase: w41A variant product with t-butyl peroxide==
-[[2wd4]] 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=2WD4 OCA].
+<StructureSection load='2wd4' size='340' side='right'caption='[[2wd4]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2wd4]] 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=2WD4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2WD4 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]] 1.4&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=FE:FE+(III)+ION'>FE</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=TBV:3-[2-[[3-(2-CARBOXYETHYL)-5-[[3-ETHENYL-4-METHYL-5-[(2-METHYLPROPAN-2-YL)OXY]-1H-PYRROL-2-YL]METHYL]-4-METHYL-1H-PYRROL+-2-YL]METHYL]-5-[(Z)-(4-ETHENYL-3-METHYL-5-OXO-PYRROL-2-YLIDENE)METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC+ACID'>TBV</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=2wd4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2wd4 OCA], [https://pdbe.org/2wd4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2wd4 RCSB], [https://www.ebi.ac.uk/pdbsum/2wd4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2wd4 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/wd/2wd4_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=2wd4 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The heme peroxidases and heme oxygenase enzymes share a common heme prosthetic group but catalyse fundamentally different reactions, the first being H2O2-dependent oxidation of substrate using an oxidised Compound I intermediate, the second O2-dependent degradation of heme. It has been proposed that these enzymes utilise a common reaction intermediate, a ferric hydroperoxide species, that sits at a crossroads in the mechanism and beyond which there are two mutually exclusive mechanistic pathways. Here, we present evidence to support this proposal in a heme peroxidase. Hence, we describe kinetic data for a variant of ascorbate peroxidase (W41A) which reacts slowly with t-butylhydroperoxide and does not form the usual peroxidase Compound I intermediate; instead, structural data show that a product is formed in which the heme has been cleaved at the alpha-meso position, analogous to the heme oxygenase mechanism. We interpret this to mean that the Compound I (peroxidase) pathway is shut down, so that instead the reaction intermediate diverts through the alternative (heme oxygenase) route. A mechanism for formation of the product is proposed and discussed in the light of what is known about the heme oxygenase reaction mechanism.
+Evidence for Heme Oxygenase Activity in a Heme Peroxidase.,Raven E, Badyal S, Eaton G, Mistry S, Pipirou Z, Basran J, Metcalfe C, Gumiero A, Handa S, Moody P Biochemistry. 2009 Mar 23. PMID:19309109<ref>PMID:19309109</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2wd4" style="background-color:#fffaf0;"></div>
 ==See Also==
-*[[Ascorbate peroxidase|Ascorbate peroxidase]]
+*[[Ascorbate peroxidase 3D structures|Ascorbate peroxidase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:019309109</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Glycine max]]
-[[Category: L-ascorbate peroxidase]]
+[[Category: Large Structures]]
-[[Category: Badyal, S K.]]
+[[Category: Badyal SK]]
-[[Category: Gumiero, A.]]
+[[Category: Gumiero A]]
-[[Category: Metcalfe, C L.]]
+[[Category: Metcalfe CL]]
-[[Category: Moody, P C.E.]]
+[[Category: Moody PCE]]
-[[Category: Raven, E L.]]
+[[Category: Raven EL]]
-[[Category: Heme peroxidase]]
-[[Category: Oxidoreductase]]
-[[Category: Peroxide scavenge]]
-[[Category: Tert-butyl peroxide]]