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New page: left|200px<br /> <applet load="3cyt" size="450" color="white" frame="true" align="right" spinBox="true" caption="3cyt, resolution 1.8Å" /> '''REDOX CONFORMATION C... |
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== | ==REDOX CONFORMATION CHANGES IN REFINED TUNA CYTOCHROME C== | ||
Tuna ferrocytochrome c and ferricytochrome c have been refined | <StructureSection load='3cyt' size='340' side='right'caption='[[3cyt]], [[Resolution|resolution]] 1.80Å' scene=''> | ||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[3cyt]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Albacore Albacore]. This structure supersedes the now removed PDB entry [http://oca.weizmann.ac.il/oca-bin/send-pdb?obs=1&id=1cyt 1cyt]. The December 2002 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Cytochrome c'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2002_12 10.2210/rcsb_pdb/mom_2002_12]. The May 2007 RCSB PDB [https://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/index.html Molecule of the Month] feature on ''Aconitase and Iron Regulatory Protein 1'' by David S. Goodsell is [https://dx.doi.org/10.2210/rcsb_pdb/mom_2007_5 10.2210/rcsb_pdb/mom_2007_5]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3CYT OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3CYT 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></td></tr> | |||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</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=3cyt FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3cyt OCA], [https://pdbe.org/3cyt PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3cyt RCSB], [https://www.ebi.ac.uk/pdbsum/3cyt PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3cyt ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[[https://www.uniprot.org/uniprot/CYC_THUAA CYC_THUAA]] 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. | |||
== 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/cy/3cyt_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/main_output.php?pdb_ID=3cyt ConSurf]. | |||
<div style="clear:both"></div> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Tuna ferrocytochrome c and ferricytochrome c have been refined independently at high resolution (1.5 A and 1.8 A) to crystallographic residual errors of 17.3% and 20.8%, respectively. Small but significant conformational differences are seen surrounding a buried water molecule that is hydrogen bonded to Asn-52, Tyr-67, and Thr-78. In the oxidized state, this water molecule is 1.0 A closer to the heme and the heme has moved 0.15 A out of its heme crevice; both changes lead to a more polar microenvironment for the heme. Chemical modification studies, patterns of evolutionary conservatism, structural differences in bacterial cytochromes, and x-ray studies all agree that the "active site" for cytochrome c is bounded by lysines 8, 13,27, 72, 79, 86, and 87 (thus containing the evolutionary conservative 72-87 loop) and has the buried water molecule just below its surface and the opening of the heme crevice slightly to one side. | |||
Redox conformation changes in refined tuna cytochrome c.,Takano T, Dickerson RE Proc Natl Acad Sci U S A. 1980 Nov;77(11):6371-5. PMID:6256733<ref>PMID:6256733</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 3cyt" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Cytochrome C 3D structures|Cytochrome C 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Aconitase and Iron Regulatory Protein 1]] | [[Category: Aconitase and Iron Regulatory Protein 1]] | ||
[[Category: Albacore]] | |||
[[Category: Cytochrome c]] | [[Category: Cytochrome c]] | ||
[[Category: | [[Category: Large Structures]] | ||
[[Category: | [[Category: RCSB PDB Molecule of the Month]] | ||
[[Category: Takano, T | [[Category: Takano, T]] | ||
Latest revision as of 17:51, 3 March 2021
REDOX CONFORMATION CHANGES IN REFINED TUNA CYTOCHROME CREDOX CONFORMATION CHANGES IN REFINED TUNA CYTOCHROME C
Structural highlights
Function[CYC_THUAA] 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. 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 PubMedTuna ferrocytochrome c and ferricytochrome c have been refined independently at high resolution (1.5 A and 1.8 A) to crystallographic residual errors of 17.3% and 20.8%, respectively. Small but significant conformational differences are seen surrounding a buried water molecule that is hydrogen bonded to Asn-52, Tyr-67, and Thr-78. In the oxidized state, this water molecule is 1.0 A closer to the heme and the heme has moved 0.15 A out of its heme crevice; both changes lead to a more polar microenvironment for the heme. Chemical modification studies, patterns of evolutionary conservatism, structural differences in bacterial cytochromes, and x-ray studies all agree that the "active site" for cytochrome c is bounded by lysines 8, 13,27, 72, 79, 86, and 87 (thus containing the evolutionary conservative 72-87 loop) and has the buried water molecule just below its surface and the opening of the heme crevice slightly to one side. Redox conformation changes in refined tuna cytochrome c.,Takano T, Dickerson RE Proc Natl Acad Sci U S A. 1980 Nov;77(11):6371-5. PMID:6256733[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. See AlsoReferences |
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