2wd4
From Proteopedia
(Difference between revisions)
(New page: '''Unreleased structure''' The entry 2wd4 is ON HOLD until sometime in the future Authors: Badyal, S.K., Metcalfe, C.L., Gumiero, A., Raven, E.L., E Moody, P.C. Description: Ascorbate ...) |
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| - | '''Unreleased structure''' | ||
| - | + | ==Ascorbate Peroxidase as a heme oxygenase: w41A variant product with t-butyl peroxide== | |
| + | <StructureSection load='2wd4' size='340' side='right'caption='[[2wd4]], [[Resolution|resolution]] 1.40Å' 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]] 1.4Å</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®/PubMed®, 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 3D structures|Ascorbate peroxidase 3D structures]] | ||
| + | == References == | ||
| + | <references/> | ||
| + | __TOC__ | ||
| + | </StructureSection> | ||
| + | [[Category: Glycine max]] | ||
| + | [[Category: Large Structures]] | ||
| + | [[Category: Badyal SK]] | ||
| + | [[Category: Gumiero A]] | ||
| + | [[Category: Metcalfe CL]] | ||
| + | [[Category: Moody PCE]] | ||
| + | [[Category: Raven EL]] | ||
Current revision
Ascorbate Peroxidase as a heme oxygenase: w41A variant product with t-butyl peroxide
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