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2vly

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(New page: 200px<br /><applet load="2vly" size="350" color="white" frame="true" align="right" spinBox="true" caption="2vly, resolution 1.60&Aring;" /> '''CRYSTAL STRUCTURE OF...)
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[[Image:2vly.jpg|left|200px]]<br /><applet load="2vly" size="350" color="white" frame="true" align="right" spinBox="true"
 
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caption="2vly, resolution 1.60&Aring;" />
 
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'''CRYSTAL STRUCTURE OF MYOGLOBIN COMPOUND III (RADIATION-INDUCED)'''<br />
 
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==Overview==
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==Crystal structure of myoglobin compound III (radiation-induced)==
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The biological conversions of O(2) and peroxides to water as well as, certain incorporations of oxygen atoms into small organic molecules can be, catalyzed by metal ions in different clusters or cofactors. The catalytic, cycle of these reactions passes through similar metal-based complexes in, which one oxygen- or peroxide-derived oxygen atom is coordinated to an, oxidized form of the catalytic metal center. In haem-based peroxidases or, oxygenases the ferryl (Fe(IV)O) form is important in compound I and, compound II, which are two and one oxidation equivalents higher than the, ferric (Fe(III)) form, respectively. In this study we report the 1.35 A, structure of a compound II model protein, obtained by reacting hydrogen, peroxide with ferric myoglobin at pH 5.2. The molecular geometry is, virtually unchanged compared to the ferric form, indicating that these, reactive intermediates do not undergo large structural changes. It is, further suggested that at low pH the dominating compound II resonance form, is a hydroxyl radical ferric iron rather than an oxo-ferryl form, based on, the short hydrogen bonding to the distal histidine (2.70 A) and the Fe...O, distance. The 1.92 A Fe...O distance is in agreement with an EXAFS study, of compound II in horseradish peroxidase.
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<StructureSection load='2vly' size='340' side='right'caption='[[2vly]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[2vly]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VLY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VLY FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.6&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2vly FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vly OCA], [https://pdbe.org/2vly PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vly RCSB], [https://www.ebi.ac.uk/pdbsum/2vly PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vly ProSAT]</span></td></tr>
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/MYG_HORSE MYG_HORSE] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/vl/2vly_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=2vly ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Myoglobin has the ability to react with hydrogen peroxide, generating high-valent complexes similar to peroxidases (compounds I and II), and in the presence of excess hydrogen peroxide a third intermediate, compound III, with an oxymyoglobin-type structure is generated from compound II. The compound III is, however, easily one-electron reduced to peroxymyoglobin by synchrotron radiation during crystallographic data collection. We have generated and solved the 1.30 A (1 A=0.1 nm) resolution crystal structure of the peroxymyoglobin intermediate, which is isoelectric to compound 0 and has a Fe-O distance of 1.8 A and O-O bond of 1.3 A in accordance with a Fe(II)-O-O- (or Fe(III)-O-O2-) structure. The generation of the peroxy intermediate through reduction of compound III by X-rays shows the importance of using single-crystal microspectrophotometry when doing crystallography on metalloproteins. After having collected crystallographic data on a peroxy-generated myoglobin crystal, we were able (by a short annealing) to break the O-O bond leading to formation of compound II. These results indicate that the cryoradiolytic-generated peroxymyoglobin is biologically relevant through its conversion into compound II upon heating. Additionally, we have observed that the Xe1 site is occupied by a water molecule, which might be the leaving group in the compound II to compound III reaction.
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==About this Structure==
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The crystal structure of peroxymyoglobin generated through cryoradiolytic reduction of myoglobin compound III during data collection.,Hersleth HP, Hsiao YW, Ryde U, Gorbitz CH, Andersson KK Biochem J. 2008 Jun 1;412(2):257-64. PMID:18215120<ref>PMID:18215120</ref>
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2VLY is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus] with <scene name='pdbligand=SO4:'>SO4</scene>, <scene name='pdbligand=HEM:'>HEM</scene>, <scene name='pdbligand=OXY:'>OXY</scene>, <scene name='pdbligand=PEO:'>PEO</scene> and <scene name='pdbligand=GOL:'>GOL</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. Known structural/functional Sites: <scene name='pdbsite=AC1:Hem Binding Site For Residue A 1154'>AC1</scene>, <scene name='pdbsite=AC2:Oxy Binding Site For Residue A 1155'>AC2</scene>, <scene name='pdbsite=AC3:So4 Binding Site For Residue A 1156'>AC3</scene>, <scene name='pdbsite=AC4:So4 Binding Site For Residue A 1157'>AC4</scene>, <scene name='pdbsite=AC5:Gol Binding Site For Residue A 1158'>AC5</scene>, <scene name='pdbsite=AC6:Gol Binding Site For Residue A 1159'>AC6</scene>, <scene name='pdbsite=AC7:Peo Binding Site For Residue A 1160'>AC7</scene> and <scene name='pdbsite=AC8:Peo Binding Site For Residue A 1161'>AC8</scene>. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VLY OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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An iron hydroxide moiety in the 1.35 A resolution structure of hydrogen peroxide derived myoglobin compound II at pH 5.2., Hersleth HP, Dalhus B, Gorbitz CH, Andersson KK, J Biol Inorg Chem. 2002 Mar;7(3):299-304. Epub 2001 Oct 11. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11935353 11935353]
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</div>
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[[Category: Equus caballus]]
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<div class="pdbe-citations 2vly" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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[[Category: Andersson, K.K.]]
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[[Category: Gorbitz, C.H.]]
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[[Category: Hersleth, H.P.]]
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[[Category: GOL]]
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[[Category: HEM]]
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[[Category: OXY]]
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[[Category: PEO]]
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[[Category: SO4]]
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[[Category: ferryl]]
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[[Category: haem]]
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[[Category: heme]]
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[[Category: iron]]
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[[Category: metal-binding]]
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[[Category: monooxygenase]]
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[[Category: muscle protein]]
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[[Category: oxygen activation]]
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[[Category: oxygen storage/transport]]
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[[Category: oxygen transport]]
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[[Category: peroxidase]]
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[[Category: radiolytic- reduction]]
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[[Category: reaction intermediate]]
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[[Category: transport]]
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[[Category: x-ray-induced-photoreduction]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Jan 31 11:02:29 2008''
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==See Also==
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*[[Myoglobin 3D structures|Myoglobin 3D structures]]
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*[[Phosphoinositide 3-kinase 3D structures|Phosphoinositide 3-kinase 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Equus caballus]]
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[[Category: Large Structures]]
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[[Category: Andersson KK]]
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[[Category: Gorbitz CH]]
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[[Category: Hersleth H-P]]

Current revision

Crystal structure of myoglobin compound III (radiation-induced)

PDB ID 2vly

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