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5t7h

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Crystal structure of dimeric yeast iso-1-cytochrome C with CYMAL6

Structural highlights

5t7h is a 4 chain structure with sequence from Saccharomyces cerevisiae S288C. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.003Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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.

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

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/5t7h"

@@ Line 3: / Line 3: @@
 <StructureSection load='5t7h' size='340' side='right'caption='[[5t7h]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5t7h]] is a 4 chain structure with sequence from [https://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=5T7H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5T7H FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5t7h]] is a 4 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=5T7H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5T7H FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZE7:6-CYCLOHEXYLHEXAN-1-OL'>ZE7</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]] 2.003&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">CYC1, YJR048W, J1653 ([https://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=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZE7:6-CYCLOHEXYLHEXAN-1-OL'>ZE7</scene></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=5t7h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5t7h OCA], [https://pdbe.org/5t7h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5t7h RCSB], [https://www.ebi.ac.uk/pdbsum/5t7h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5t7h ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[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.
+[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;">
 == Publication Abstract from PubMed ==
@@ Line 26: / Line 26: @@
 __TOC__
 </StructureSection>
-[[Category: Baker's yeast]]
 [[Category: Large Structures]]
-[[Category: Bowler, B E]]
+[[Category: Saccharomyces cerevisiae S288C]]
-[[Category: Mcclelland, L]]
+[[Category: Bowler BE]]
-[[Category: Mou, T C]]
+[[Category: Mcclelland L]]
-[[Category: Sprang, S R]]
+[[Category: Mou TC]]
-[[Category: Cymal6]]
+[[Category: Sprang SR]]
-[[Category: Cytochrome c]]
-[[Category: Electron transport]]
-[[Category: Peroxidase activity]]

5t7h

From Proteopedia

Current revision

Crystal structure of dimeric yeast iso-1-cytochrome C with CYMAL6

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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