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| | <StructureSection load='6h08' size='340' side='right'caption='[[6h08]], [[Resolution|resolution]] 1.90Å' scene=''> | | <StructureSection load='6h08' size='340' side='right'caption='[[6h08]], [[Resolution|resolution]] 1.90Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[6h08]] is a 3 chain structure with sequence from [http://en.wikipedia.org/wiki/Atcc_18824 Atcc 18824]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6H08 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6H08 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[6h08]] is a 3 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=6H08 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6H08 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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]] 1.9Å</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MHS:N1-METHYLATED+HISTIDINE'>MHS</scene></td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CO:COBALT+(II)+ION'>CO</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MHS:N1-METHYLATED+HISTIDINE'>MHS</scene>, <scene name='pdbligand=MN:MANGANESE+(II)+ION'>MN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=4932 ATCC 18824])</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=6h08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6h08 OCA], [https://pdbe.org/6h08 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6h08 RCSB], [https://www.ebi.ac.uk/pdbsum/6h08 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6h08 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://proteopedia.org/fgij/fg.htm?mol=6h08 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6h08 OCA], [http://pdbe.org/6h08 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6h08 RCSB], [http://www.ebi.ac.uk/pdbsum/6h08 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6h08 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;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
| Line 21: |
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| | </div> | | </div> |
| | <div class="pdbe-citations 6h08" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 6h08" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Cytochrome c peroxidase 3D structures|Cytochrome c peroxidase 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Atcc 18824]] | |
| - | [[Category: Cytochrome-c peroxidase]] | |
| | [[Category: Large Structures]] | | [[Category: Large Structures]] |
| - | [[Category: Green, A P]] | |
| - | [[Category: Levy, C]] | |
| - | [[Category: Ortmayer, M]] | |
| - | [[Category: Engineered cytochrome c peroxidase]] | |
| - | [[Category: Me-hi]] | |
| - | [[Category: Oxidoreductase]] | |
| - | [[Category: Proximal ligand]] | |
| | [[Category: Saccharomyces cerevisiae]] | | [[Category: Saccharomyces cerevisiae]] |
| | + | [[Category: Green AP]] |
| | + | [[Category: Levy C]] |
| | + | [[Category: Ortmayer M]] |
| Structural highlights
6h08 is a 3 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 1.9Å |
| 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.
Publication Abstract from PubMed
Nature employs a limited number of genetically encoded axial ligands to control diverse heme enzyme activities. Deciphering the functional significance of these ligands requires a quantitative understanding of how their electron-donating capabilities modulate the structures and reactivities of the iconic ferryl intermediates compounds I and II. However, probing these relationships experimentally has proven to be challenging as ligand substitutions accessible via conventional mutagenesis do not allow fine tuning of electron donation and typically abolish catalytic function. Here, we exploit engineered translation components to replace the histidine ligand of cytochrome c peroxidase (CcP) by a less electron-donating N delta-methyl histidine (Me-His) with little effect on the enzyme structure. The rate of formation (k 1) and the reactivity (k 2) of compound I are unaffected by ligand substitution. In contrast, proton-coupled electron transfer to compound II (k 3) is 10-fold slower in CcP Me-His, providing a direct link between electron donation and compound II reactivity, which can be explained by weaker electron donation from the Me-His ligand ("the push") affording an electron-deficient ferryl oxygen with reduced proton affinity ("the pull"). The deleterious effects of the Me-His ligand can be fully compensated by introducing a W51F mutation designed to increase "the pull" by removing a hydrogen bond to the ferryl oxygen. Analogous substitutions in ascorbate peroxidase lead to similar activity trends to those observed in CcP, suggesting that a common mechanistic strategy is employed by enzymes using distinct electron transfer pathways. Our study highlights how noncanonical active site substitutions can be used to directly probe and deconstruct highly evolved bioinorganic mechanisms.
Rewiring the "Push-Pull" Catalytic Machinery of a Heme Enzyme Using an Expanded Genetic Code.,Ortmayer M, Fisher K, Basran J, Wolde-Michael EM, Heyes DJ, Levy C, Lovelock SL, Anderson JLR, Raven EL, Hay S, Rigby SEJ, Green AP ACS Catal. 2020 Feb 21;10(4):2735-2746. doi: 10.1021/acscatal.9b05129. Epub 2020 , Jan 29. PMID:32550044[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ Ortmayer M, Fisher K, Basran J, Wolde-Michael EM, Heyes DJ, Levy C, Lovelock SL, Anderson JLR, Raven EL, Hay S, Rigby SEJ, Green AP. Rewiring the "Push-Pull" Catalytic Machinery of a Heme Enzyme Using an Expanded Genetic Code. ACS Catal. 2020 Feb 21;10(4):2735-2746. doi: 10.1021/acscatal.9b05129. Epub 2020 , Jan 29. PMID:32550044 doi:http://dx.doi.org/10.1021/acscatal.9b05129
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