2vm0

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[[Image:2vm0.jpg|left|200px]]
 
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{{Structure
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==Crystal structure of radiation-induced myoglobin compound II generated after annealing of peroxymyoglobin==
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|PDB= 2vm0 |SIZE=350|CAPTION= <scene name='initialview01'>2vm0</scene>, resolution 1.60&Aring;
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<StructureSection load='2vm0' size='340' side='right'caption='[[2vm0]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
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|SITE= <scene name='pdbsite=AC1:Hem+Binding+Site+For+Residue+A+1154'>AC1</scene>, <scene name='pdbsite=AC2:Hyd+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:Peo+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>
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=HYD:HYDROXY+GROUP'>HYD</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>
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<table><tr><td colspan='2'>[[2vm0]] 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=2VM0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2VM0 FirstGlance]. <br>
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|ACTIVITY=
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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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|GENE=
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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=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=PEO:HYDROGEN+PEROXIDE'>PEO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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|DOMAIN=<span class='plainlinks'>[http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=cd01040 globin]</span>
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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=2vm0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vm0 OCA], [https://pdbe.org/2vm0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2vm0 RCSB], [https://www.ebi.ac.uk/pdbsum/2vm0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2vm0 ProSAT]</span></td></tr>
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|RELATEDENTRY=[[1azi|1AZI]], [[1dwr|1DWR]], [[1dwt|1DWT]], [[1gjn|1GJN]], [[1hrm|1HRM]], [[1npf|1NPF]], [[1npg|1NPG]], [[1nz2|1NZ2]], [[1nz3|1NZ3]], [[1rse|1RSE]], [[1yma|1YMA]], [[1ymb|1YMB]], [[2frf|2FRF]], [[2frj|2FRJ]], [[2frk|2FRK]], [[2in4|2IN4]], [[2v1e|2V1E]], [[2v1f|2V1F]], [[2v1g|2V1G]], [[2v1h|2V1H]], [[2v1i|2V1I]], [[2v1j|2V1J]], [[1bje|1BJE]], [[1dws|1DWS]], [[1hsy|1HSY]], [[1nz4|1NZ4]], [[1nz5|1NZ5]], [[1wla|1WLA]], [[1xch|1XCH]], [[1ymc|1YMC]], [[2fri|2FRI]], [[2v1k|2V1K]], [[2vlx|2VLX]], [[2vly|2VLY]], [[2vlz|2VLZ]]
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2vm0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2vm0 OCA], [http://www.ebi.ac.uk/pdbsum/2vm0 PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2vm0 RCSB]</span>
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== Function ==
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}}
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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/vm/2vm0_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=2vm0 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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'''CRYSTAL STRUCTURE OF RADIATION-INDUCED MYOGLOBIN COMPOUND II GENERATED AFTER ANNEALING OF PEROXYMYOGLOBIN'''
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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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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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<div class="pdbe-citations 2vm0" style="background-color:#fffaf0;"></div>
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==Overview==
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==See Also==
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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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*[[Myoglobin 3D structures|Myoglobin 3D structures]]
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== References ==
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==About this Structure==
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<references/>
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2VM0 is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Equus_caballus Equus caballus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2VM0 OCA].
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__TOC__
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</StructureSection>
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==Reference==
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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://www.ncbi.nlm.nih.gov/pubmed/11935353 11935353]
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[[Category: Equus caballus]]
[[Category: Equus caballus]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Andersson, K K.]]
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[[Category: Andersson KK]]
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[[Category: Gorbitz, C H.]]
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[[Category: Gorbitz CH]]
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[[Category: Hersleth, H P.]]
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[[Category: Hersleth H-P]]
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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 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 Wed Apr 2 11:32:33 2008''
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Current revision

Crystal structure of radiation-induced myoglobin compound II generated after annealing of peroxymyoglobin

PDB ID 2vm0

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