3m2h: Difference between revisions

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[[Image:3m2h.png|left|200px]]
==Crystallographic and Single Crystal Spectral Analysis of the Peroxidase Ferryl Intermediate==
<StructureSection load='3m2h' size='340' side='right' caption='[[3m2h]], [[Resolution|resolution]] 1.40&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[3m2h]] 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=3M2H OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3M2H 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>
<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]], [[3m2b|3m2b]], [[3m2c|3m2c]], [[3m2d|3m2d]], [[3m2e|3m2e]], [[3m2f|3m2f]], [[3m2g|3m2g]], [[3m2i|3m2i]]</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='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=3m2h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3m2h OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3m2h RCSB], [http://www.ebi.ac.uk/pdbsum/3m2h PDBsum]</span></td></tr>
</table>
== 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/m2/3m2h_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/chain_selection.php?pdb_ID=2ata ConSurf].
<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.


{{STRUCTURE_3m2h|  PDB=3m2h  |  SCENE=  }}
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>


===Crystallographic and Single Crystal Spectral Analysis of the Peroxidase Ferryl Intermediate===
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 
</div>
{{ABSTRACT_PUBMED_20230048}}
 
==About this Structure==
[[3m2h]] 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=3M2H OCA].


==See Also==
==See Also==
*[[Cytochrome c peroxidase|Cytochrome c peroxidase]]
*[[Cytochrome c peroxidase|Cytochrome c peroxidase]]
 
== References ==
==Reference==
<references/>
<ref group="xtra">PMID:020230048</ref><references group="xtra"/>
__TOC__
</StructureSection>
[[Category: Cytochrome-c peroxidase]]
[[Category: Cytochrome-c peroxidase]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Saccharomyces cerevisiae]]
[[Category: Meharenna, Y T.]]
[[Category: Meharenna, Y T]]
[[Category: Poulos, T L.]]
[[Category: Poulos, T L]]
[[Category: Heme]]
[[Category: Heme]]
[[Category: Hydrogen peroxide]]
[[Category: Hydrogen peroxide]]

Revision as of 12:40, 9 December 2014

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

Structural highlights

3m2h 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.
Ligands:,
Gene:CCP, CCP1, CPO, YKR066C (Saccharomyces cerevisiae)
Activity:Cytochrome-c peroxidase, with EC number 1.11.1.5
Resources:FirstGlance, OCA, RCSB, PDBsum

Evolutionary Conservation

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

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[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

See Also

References

  1. ↑ Meharenna YT, Doukov T, Li H, Soltis SM, Poulos TL. Crystallographic and single-crystal spectral analysis of the peroxidase ferryl intermediate. Biochemistry. 2010 Apr 13;49(14):2984-6. PMID:20230048 doi:10.1021/bi100238r

3m2h, resolution 1.40Å

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