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| <StructureSection load='5ejt' size='340' side='right'caption='[[5ejt]], [[Resolution|resolution]] 1.55Å' scene=''> | | <StructureSection load='5ejt' size='340' side='right'caption='[[5ejt]], [[Resolution|resolution]] 1.55Å' scene=''> |
| == Structural highlights == | | == Structural highlights == |
| <table><tr><td colspan='2'>[[5ejt]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Baker's_yeast Baker's yeast]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EJT OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5EJT FirstGlance]. <br> | | <table><tr><td colspan='2'>[[5ejt]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5EJT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5EJT 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]] 1.55Å</td></tr> |
| <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[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]], [[3m2h|3m2h]], [[3m2i|3m2i]], [[5ejx|5ejx]]</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">CCP1, CCP, CPO, YKR066C ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</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=5ejt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ejt OCA], [https://pdbe.org/5ejt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5ejt RCSB], [https://www.ebi.ac.uk/pdbsum/5ejt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5ejt 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>
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| <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=5ejt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ejt OCA], [http://pdbe.org/5ejt PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ejt RCSB], [http://www.ebi.ac.uk/pdbsum/5ejt PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ejt ProSAT]</span></td></tr> | |
| </table> | | </table> |
| == Function == | | == Function == |
| [[http://www.uniprot.org/uniprot/CCPR_YEAST CCPR_YEAST]] Destroys radicals which are normally produced within the cells and which are toxic to biological systems. | | [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. |
| <div style="background-color:#fffaf0;">
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| == Publication Abstract from PubMed ==
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| The reaction of peroxides with peroxidases oxidizes the heme iron from Fe(III) to Fe(IV)=O and a porphyrin or aromatic side chain to a cationic radical. X-ray-generated hydrated electrons rapidly reduce Fe(IV), thereby requiring very short exposures using many crystals, and, even then, some reduction cannot be avoided. The new generation of X-ray free electron lasers capable of generating intense X-rays on the tenths of femtosecond time scale enables structure determination with no reduction or X-ray damage. Here, we report the 1.5-A crystal structure of cytochrome c peroxidase (CCP) compound I (CmpI) using data obtained with the Stanford Linear Coherent Light Source (LCLS). This structure is consistent with previous structures. Of particular importance is the active site water structure that can mediate the proton transfer reactions required for both CmpI formation and reduction of Fe(IV)=O to Fe(III)-OH. The structures indicate that a water molecule is ideally positioned to shuttle protons between an iron-linked oxygen and the active site catalytic His. We therefore have carried out both computational and kinetic studies to probe the reduction of Fe(IV)=O. Kinetic solvent isotope experiments show that the transfer of a single proton is critical in the peroxidase rate-limiting step, which is very likely the proton-coupled reduction of Fe(IV)=O to Fe(III)-OH. We also find that the pKa of the catalytic His substantially increases in CmpI, indicating that this active site His is the source of the proton required in the reduction of Fe(IV)=O to Fe(IV)-OH.
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| Crystal structure of the pristine peroxidase ferryl center and its relevance to proton-coupled electron transfer.,Chreifi G, Baxter EL, Doukov T, Cohen AE, McPhillips SE, Song J, Meharenna YT, Soltis SM, Poulos TL Proc Natl Acad Sci U S A. 2016 Jan 19. pii: 201521664. PMID:26787871<ref>PMID:26787871</ref>
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| From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
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| </div>
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| <div class="pdbe-citations 5ejt" style="background-color:#fffaf0;"></div>
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| ==See Also== | | ==See Also== |
| *[[Cytochrome c peroxidase 3D structures|Cytochrome c peroxidase 3D structures]] | | *[[Cytochrome c peroxidase 3D structures|Cytochrome c peroxidase 3D structures]] |
| == References ==
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| <references/>
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| __TOC__ | | __TOC__ |
| </StructureSection> | | </StructureSection> |
| [[Category: Baker's yeast]]
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| [[Category: Cytochrome-c peroxidase]]
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| [[Category: Large Structures]] | | [[Category: Large Structures]] |
| [[Category: Baxter, E L]] | | [[Category: Saccharomyces cerevisiae S288C]] |
| [[Category: Chreifi, G]] | | [[Category: Baxter EL]] |
| [[Category: Cohen, A]] | | [[Category: Chreifi G]] |
| [[Category: Doukov, T]] | | [[Category: Cohen A]] |
| [[Category: McPhillips, S]] | | [[Category: Doukov T]] |
| [[Category: Meharenna, Y T]] | | [[Category: McPhillips S]] |
| [[Category: Poulos, T L]] | | [[Category: Meharenna YT]] |
| [[Category: Soltis, S M]] | | [[Category: Poulos TL]] |
| [[Category: Song, J]] | | [[Category: Soltis SM]] |
| [[Category: Oxidoreductase]]
| | [[Category: Song J]] |