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| | ==Crystal Structure of a Domain-swapped Dimer of Yeast Iso-1-cytochrome c with omega-undecylenyl-beta-D-maltopyranoside== | | ==Crystal Structure of a Domain-swapped Dimer of Yeast Iso-1-cytochrome c with omega-undecylenyl-beta-D-maltopyranoside== |
| - | <StructureSection load='5klu' size='340' side='right' caption='[[5klu]], [[Resolution|resolution]] 1.99Å' scene=''> | + | <StructureSection load='5klu' size='340' side='right'caption='[[5klu]], [[Resolution|resolution]] 1.99Å' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[5klu]] is a 2 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=5KLU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5KLU FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[5klu]] is a 2 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=5KLU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5KLU FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=6UZ:OMEGA-UNDECYLENYL-BETA-D-MALTOPYRANOSIDE'>6UZ</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 1.99Å</td></tr> |
| - | <tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CYC1, YJR048W, J1653 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=559292 Baker's yeast])</td></tr>
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=6UZ:OMEGA-UNDECYLENYL-BETA-D-MALTOPYRANOSIDE'>6UZ</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5klu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5klu OCA], [http://pdbe.org/5klu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5klu RCSB], [http://www.ebi.ac.uk/pdbsum/5klu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5klu ProSAT]</span></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=5klu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5klu OCA], [https://pdbe.org/5klu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5klu RCSB], [https://www.ebi.ac.uk/pdbsum/5klu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5klu ProSAT]</span></td></tr> |
| | </table> | | </table> |
| | == Function == | | == Function == |
| - | [[http://www.uniprot.org/uniprot/CYC1_YEAST CYC1_YEAST]] Electron carrier protein. The oxidized form of the cytochrome c heme group can accept an electron from the heme group of the cytochrome c1 subunit of cytochrome reductase. Cytochrome c then transfers this electron to the cytochrome oxidase complex, the final protein carrier in the mitochondrial electron-transport chain. | + | [https://www.uniprot.org/uniprot/CYC1_YEAST CYC1_YEAST] Electron carrier protein. The oxidized form of the cytochrome c heme group can accept an electron from the heme group of the cytochrome c1 subunit of cytochrome reductase. Cytochrome c then transfers this electron to the cytochrome oxidase complex, the final protein carrier in the mitochondrial electron-transport chain. |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
| | == Publication Abstract from PubMed == | | == Publication Abstract from PubMed == |
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| | </div> | | </div> |
| | <div class="pdbe-citations 5klu" style="background-color:#fffaf0;"></div> | | <div class="pdbe-citations 5klu" style="background-color:#fffaf0;"></div> |
| | + | |
| | + | ==See Also== |
| | + | *[[Cytochrome C 3D structures|Cytochrome C 3D structures]] |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Baker's yeast]] | + | [[Category: Large Structures]] |
| - | [[Category: Bowler, B E]] | + | [[Category: Saccharomyces cerevisiae S288C]] |
| - | [[Category: Whitby, F G]] | + | [[Category: Bowler BE]] |
| - | [[Category: Electron transport]] | + | [[Category: Whitby FG]] |
| - | [[Category: Electron transport apoptosis lipid binding]]
| + | |
| Structural highlights
Function
CYC1_YEAST Electron carrier protein. The oxidized form of the cytochrome c heme group can accept an electron from the heme group of the cytochrome c1 subunit of cytochrome reductase. Cytochrome c then transfers this electron to the cytochrome oxidase complex, the final protein carrier in the mitochondrial electron-transport chain.
Publication Abstract from PubMed
Cytochrome c can acquire peroxidase activity when it binds to cardiolipin in mitochondrial membranes. The resulting oxygenation of cardiolipin by cytochrome c provides an early signal for the onset of apoptosis. The structure of this enzyme-substrate complex is a matter of considerable debate. We present three structures at 1.7-2.0 A resolution of a domain-swapped dimer of yeast iso-1-cytochrome c with the detergents, CYMAL-5, CYMAL-6, and omega-undecylenyl-beta-d-maltopyranoside, bound in a channel that places the hydrocarbon moieties of these detergents next to the heme. The heme is poised for peroxidase activity with water bound in place of Met80, which serves as the axial heme ligand when cytochrome c functions as an electron carrier. The hydroxyl group of Tyr67 sits 3.6-4.0 A from the nearest carbon of the detergents, positioned to act as a relay in radical abstraction during peroxidase activity. Docking studies with linoleic acid, the most common fatty acid component of cardiolipin, show that C11 of linoleic acid can sit adjacent to Tyr67 and the heme, consistent with the oxygenation pattern observed in lipidomics studies. The well-defined hydrocarbon binding pocket provides atomic resolution evidence for the extended lipid anchorage model for cytochrome c/cardiolipin binding. Dimer dissociation/association kinetics for yeast versus equine cytochrome c indicate that formation of mammalian cytochrome c dimers in vivo would require catalysis. However, the dimer structure shows that only a modest deformation of monomeric cytochrome c would suffice to form the hydrocarbon binding site occupied by these detergents.
Cytochrome c Can Form a Well-Defined Binding Pocket for Hydrocarbons.,McClelland LJ, Steele HB, Whitby FG, Mou TC, Holley D, Ross JB, Sprang SR, Bowler BE J Am Chem Soc. 2016 Dec 28;138(51):16770-16778. doi: 10.1021/jacs.6b10745. Epub, 2016 Dec 19. PMID:27990813[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
See Also
References
- ↑ McClelland LJ, Steele HB, Whitby FG, Mou TC, Holley D, Ross JB, Sprang SR, Bowler BE. Cytochrome c Can Form a Well-Defined Binding Pocket for Hydrocarbons. J Am Chem Soc. 2016 Dec 28;138(51):16770-16778. doi: 10.1021/jacs.6b10745. Epub, 2016 Dec 19. PMID:27990813 doi:http://dx.doi.org/10.1021/jacs.6b10745
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