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==Crystallographic and Single Crystal Spectral Analysis of the Peroxidase Ferryl Intermediate==
==Crystallographic and Single Crystal Spectral Analysis of the Peroxidase Ferryl Intermediate==
<StructureSection load='3m2b' size='340' side='right' caption='[[3m2b]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
<StructureSection load='3m2b' size='340' side='right'caption='[[3m2b]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[3m2b]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M2B OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3M2B FirstGlance]. <br>
<table><tr><td colspan='2'>[[3m2b]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3M2B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3M2B FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1dso|1dso]], [[2v23|2v23]], [[1dsg|1dsg]], [[1zby|1zby]], [[5ccp|5ccp]], [[3e2n|3e2n]], [[3e2o|3e2o]], [[3m23|3m23]], [[3m25|3m25]], [[3m26|3m26]], [[3m27|3m27]], [[3m28|3m28]], [[3m29|3m29]], [[3m2a|3m2a]], [[3m2c|3m2c]], [[3m2d|3m2d]], [[3m2e|3m2e]], [[3m2f|3m2f]], [[3m2g|3m2g]], [[3m2h|3m2h]], [[3m2i|3m2i]]</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CCP, CCP1, CPO, YKR066C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=4932 Saccharomyces cerevisiae])</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=3m2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m2b OCA], [https://pdbe.org/3m2b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3m2b RCSB], [https://www.ebi.ac.uk/pdbsum/3m2b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3m2b ProSAT]</span></td></tr>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] </span></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3m2b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m2b OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3m2b RCSB], [http://www.ebi.ac.uk/pdbsum/3m2b PDBsum]</span></td></tr>
</table>
</table>
== Function ==
[https://www.uniprot.org/uniprot/CCPR_YEAST CCPR_YEAST] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.
== Evolutionary Conservation ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m2/3m2b_consurf.spt"</scriptWhenChecked>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/m2/3m2b_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </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/chain_selection.php?pdb_ID=2ata ConSurf].
</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=3m2b ConSurf].
<div style="clear:both"></div>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The ferryl [Fe(IV)O] intermediate is important in many heme enzymes, and thus, the precise nature of the Fe(IV)-O bond is critical in understanding enzymatic mechanisms. The 1.40 A crystal structure of cytochrome c peroxidase Compound I has been determined as a function of X-ray dose while the visible spectrum was being monitored. The Fe-O bond increases in length from 1.73 A in the low-X-ray dose structure to 1.90 A in the high-dose structure. The low-dose structure correlates well with an Fe(IV) horizontal lineO bond, while we postulate that the high-dose structure is the cryo-trapped Fe(III)-OH species previously thought to be an Fe(IV)-OH species.
Crystallographic and single-crystal spectral analysis of the peroxidase ferryl intermediate.,Meharenna YT, Doukov T, Li H, Soltis SM, Poulos TL Biochemistry. 2010 Apr 13;49(14):2984-6. PMID:20230048<ref>PMID:20230048</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[Cytochrome c peroxidase|Cytochrome c peroxidase]]
*[[Cytochrome c peroxidase 3D structures|Cytochrome c peroxidase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Cytochrome-c peroxidase]]
[[Category: Large Structures]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Meharenna, Y T]]
[[Category: Meharenna YT]]
[[Category: Poulos, T L]]
[[Category: Poulos TL]]
[[Category: Heme]]
[[Category: Hydrogen peroxide]]
[[Category: Iron]]
[[Category: Metal-binding]]
[[Category: Mitochondrion]]
[[Category: Oxidoreductase]]
[[Category: Peroxidase]]

Latest revision as of 13:23, 21 February 2024

Crystallographic and Single Crystal Spectral Analysis of the Peroxidase Ferryl IntermediateCrystallographic and Single Crystal Spectral Analysis of the Peroxidase Ferryl Intermediate

Structural highlights

3m2b is a 1 chain structure with sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.4Å
Ligands:,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CCPR_YEAST Destroys radicals which are normally produced within the cells and which are toxic to biological systems.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

3m2b, resolution 1.40Å

Drag the structure with the mouse to rotate

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OCA
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