2v1f: Difference between revisions

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[[Image:2v1f.gif|left|200px]]


{{Structure
==Crystal structure of radiation-induced myoglobin compound II - intermediate H at pH 8.7==
|PDB= 2v1f |SIZE=350|CAPTION= <scene name='initialview01'>2v1f</scene>, resolution 1.20&Aring;
<StructureSection load='2v1f' size='340' side='right'caption='[[2v1f]], [[Resolution|resolution]] 1.20&Aring;' scene=''>
|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:Gol+Binding+Site+For+Residue+A+1159'>AC6</scene>, <scene name='pdbsite=AC7:Gol+Binding+Site+For+Residue+A+1160'>AC7</scene> and <scene name='pdbsite=AC8:Gol+Binding+Site+For+Residue+A+1161'>AC8</scene>
== Structural highlights ==
|LIGAND= <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=HYD:HYDROXY+GROUP'>HYD</scene> and <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
<table><tr><td colspan='2'>[[2v1f]] 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=2V1F OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2V1F FirstGlance]. <br>
|ACTIVITY=  
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.2&#8491;</td></tr>
|GENE=  
<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=SO4:SULFATE+ION'>SO4</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=2v1f FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2v1f OCA], [https://pdbe.org/2v1f PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2v1f RCSB], [https://www.ebi.ac.uk/pdbsum/2v1f PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2v1f ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/MYG_HORSE MYG_HORSE] Serves as a reserve supply of oxygen and facilitates the movement of oxygen within muscles.
== 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/v1/2v1f_consurf.spt"</scriptWhenChecked>
    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=2v1f ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
High resolution crystal structures of myoglobin in the pH range 5.2-8.7 have been used as models for the peroxide-derived compound II intermediates in heme peroxidases and oxygenases. The observed Fe-O bond length (1.86-1.90 A) is consistent with that of a single bond. The compound II state of myoglobin in crystals was controlled by single-crystal microspectrophotometry before and after synchrotron data collection. We observe some radiation-induced changes in both compound II (resulting in intermediate H) and in the resting ferric state of myoglobin. These radiation-induced states are quite unstable, and compound II and ferric myoglobin are immediately regenerated through a short heating above the glass transition temperature (&lt;1 s) of the crystals. It is unclear how this influences our compound II structures compared with the unaffected compound II, but some crystallographic data suggest that the influence on the Fe-O bond distance is minimal. Based on our crystallographic and spectroscopic data we suggest that for myoglobin the compound II intermediate consists of an Fe(IV)-O species with a single bond. The presence of Fe(IV) is indicated by a small isomer shift of delta = 0.07 mm/s from Mossbauer spectroscopy. Earlier quantum refinements (crystallographic refinement where the molecular-mechanics potential is replaced by a quantum chemical calculation) and density functional theory calculations suggest that this intermediate H species is protonated.


'''CRYSTAL STRUCTURE OF RADIATION-INDUCED MYOGLOBIN COMPOUND II- INTERMEDIATE H AT PH 8.7'''
Crystallographic and spectroscopic studies of peroxide-derived myoglobin compound II and occurrence of protonated FeIV O.,Hersleth HP, Uchida T, Rohr AK, Teschner T, Schunemann V, Kitagawa T, Trautwein AX, Gorbitz CH, Andersson KK J Biol Chem. 2007 Aug 10;282(32):23372-86. Epub 2007 Jun 12. PMID:17565988<ref>PMID:17565988</ref>


From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 2v1f" style="background-color:#fffaf0;"></div>


==Overview==
==See Also==
High resolution crystal structures of myoglobin in the pH range 5.2-8.7 have been used as models for the peroxide-derived compound II intermediates in heme peroxidases and oxygenases. The observed Fe-O bond length (1.86-1.90 A) is consistent with that of a single bond. The compound II state of myoglobin in crystals was controlled by single-crystal microspectrophotometry before and after synchrotron data collection. We observe some radiation-induced changes in both compound II (resulting in intermediate H) and in the resting ferric state of myoglobin. These radiation-induced states are quite unstable, and compound II and ferric myoglobin are immediately regenerated through a short heating above the glass transition temperature (&lt;1 s) of the crystals. It is unclear how this influences our compound II structures compared with the unaffected compound II, but some crystallographic data suggest that the influence on the Fe-O bond distance is minimal. Based on our crystallographic and spectroscopic data we suggest that for myoglobin the compound II intermediate consists of an Fe(IV)-O species with a single bond. The presence of Fe(IV) is indicated by a small isomer shift of delta = 0.07 mm/s from Mossbauer spectroscopy. Earlier quantum refinements (crystallographic refinement where the molecular-mechanics potential is replaced by a quantum chemical calculation) and density functional theory calculations suggest that this intermediate H species is protonated.
*[[Myoglobin 3D structures|Myoglobin 3D structures]]
 
== References ==
==About this Structure==
<references/>
2V1F 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=2V1F OCA].
__TOC__
 
</StructureSection>
==Reference==
Crystallographic and spectroscopic studies of peroxide-derived myoglobin compound II and occurrence of protonated FeIV O., Hersleth HP, Uchida T, Rohr AK, Teschner T, Schunemann V, Kitagawa T, Trautwein AX, Gorbitz CH, Andersson KK, J Biol Chem. 2007 Aug 10;282(32):23372-86. Epub 2007 Jun 12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17565988 17565988]
[[Category: Equus caballus]]
[[Category: Equus caballus]]
[[Category: Single protein]]
[[Category: Large Structures]]
[[Category: Andersson, K K.]]
[[Category: Andersson KK]]
[[Category: Gorbitz, C H.]]
[[Category: Gorbitz CH]]
[[Category: Hersleth, H P.]]
[[Category: Hersleth H-P]]
[[Category: GOL]]
[[Category: HEM]]
[[Category: HYD]]
[[Category: SO4]]
[[Category: ferryl]]
[[Category: haem]]
[[Category: heme]]
[[Category: iron]]
[[Category: metal-binding]]
[[Category: monooxygenase]]
[[Category: muscle protein]]
[[Category: oxygen activation]]
[[Category: oxygen transport]]
[[Category: peroxidase]]
[[Category: radiation]]
[[Category: reaction intermediate]]
[[Category: transport]]
 
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Retrieved from "https://proteopedia.org/2v1f"