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3cyt

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(New page: 200px<br /> <applet load="3cyt" size="450" color="white" frame="true" align="right" spinBox="true" caption="3cyt, resolution 1.8&Aring;" /> '''REDOX CONFORMATION C...)
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[[Image:3cyt.gif|left|200px]]<br />
 
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<applet load="3cyt" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="3cyt, resolution 1.8&Aring;" />
 
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'''REDOX CONFORMATION CHANGES IN REFINED TUNA CYTOCHROME C'''<br />
 
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==Overview==
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==REDOX CONFORMATION CHANGES IN REFINED TUNA CYTOCHROME C==
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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.
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<StructureSection load='3cyt' size='340' side='right'caption='[[3cyt]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
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== Structural highlights ==
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<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>
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</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>
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<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>
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<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>
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</table>
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== Function ==
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[[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.
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/cy/3cyt_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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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.
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==About this Structure==
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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>
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3CYT is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Thunnus_alalunga Thunnus alalunga] with ACE and HEM as [http://en.wikipedia.org/wiki/ligands ligands]. This structure superseeds the now removed PDB entry 1CYT. The following pages contain interesting information on the relation of 3CYT with [[http://pdb.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb89_1.html Aconitase and Iron Regulatory Protein 1]]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=3CYT OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=6256733 6256733]
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</div>
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<div class="pdbe-citations 3cyt" style="background-color:#fffaf0;"></div>
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==See Also==
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*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
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== References ==
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<references/>
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__TOC__
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</StructureSection>
[[Category: Aconitase and Iron Regulatory Protein 1]]
[[Category: Aconitase and Iron Regulatory Protein 1]]
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[[Category: Albacore]]
[[Category: Cytochrome c]]
[[Category: Cytochrome c]]
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[[Category: Single protein]]
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[[Category: Large Structures]]
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[[Category: Thunnus alalunga]]
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[[Category: RCSB PDB Molecule of the Month]]
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[[Category: Takano, T.]]
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[[Category: Takano, T]]
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[[Category: ACE]]
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[[Category: HEM]]
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[[Category: electron transport (heme protein)]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 18 09:10:11 2007''
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REDOX CONFORMATION CHANGES IN REFINED TUNA CYTOCHROME C

PDB ID 3cyt

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