3ag2: Difference between revisions

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-[[Image:3ag2.png|left|200px]]
-{{STRUCTURE_3ag2|  PDB=3ag2  |  SCENE=  }}
+==Bovine Heart Cytochrome c Oxidase in the Carbon Monoxide-bound Fully Reduced State at 100 K==
+<StructureSection load='3ag2' size='340' side='right'caption='[[3ag2]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[3ag2]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AG2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3AG2 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.802&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CDL:CARDIOLIPIN'>CDL</scene>, <scene name='pdbligand=CHD:CHOLIC+ACID'>CHD</scene>, <scene name='pdbligand=CMO:CARBON+MONOXIDE'>CMO</scene>, <scene name='pdbligand=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=CUA:DINUCLEAR+COPPER+ION'>CUA</scene>, <scene name='pdbligand=DMU:DECYL-BETA-D-MALTOPYRANOSIDE'>DMU</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=HEA:HEME-A'>HEA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=PEK:(1S)-2-{[(2-AMINOETHOXY)(HYDROXY)PHOSPHORYL]OXY}-1-[(STEAROYLOXY)METHYL]ETHYL+(5E,8E,11E,14E)-ICOSA-5,8,11,14-TETRAENOATE'>PEK</scene>, <scene name='pdbligand=PGV:(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL+(11E)-OCTADEC-11-ENOATE'>PGV</scene>, <scene name='pdbligand=PSC:(7R,17E,20E)-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-7-[(PALMITOYLOXY)METHYL]-3,5,8-TRIOXA-4-PHOSPHAHEXACOSA-17,20-DIEN-1-AMINIUM+4-OXIDE'>PSC</scene>, <scene name='pdbligand=SAC:N-ACETYL-SERINE'>SAC</scene>, <scene name='pdbligand=TGL:TRISTEAROYLGLYCEROL'>TGL</scene>, <scene name='pdbligand=TPO:PHOSPHOTHREONINE'>TPO</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=3ag2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3ag2 OCA], [https://pdbe.org/3ag2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3ag2 RCSB], [https://www.ebi.ac.uk/pdbsum/3ag2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3ag2 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/COX1_BOVIN COX1_BOVIN] Cytochrome c oxidase is the component of the respiratory chain that catalyzes the reduction of oxygen to water. Subunits 1-3 form the functional core of the enzyme complex. CO I is the catalytic subunit of the enzyme. Electrons originating in cytochrome c are transferred via the copper A center of subunit 2 and heme A of subunit 1 to the bimetallic center formed by heme A3 and copper B.
+== 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/ag/3ag2_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=3ag2 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The O(2) reduction site of cytochrome c oxidase (CcO), comprising iron (Fe(a3)) and copper (Cu(B)) ions, is probed by x-ray structural analyses of CO, NO, and CN(-) derivatives to investigate the mechanism of the complete reduction of O(2). Formation of the derivative contributes to the trigonal planar coordination of and displaces one of its three coordinated imidazole groups while a water molecule becomes hydrogen bonded to both the CN(-) ligand and the hydroxyl group of Tyr244. When O(2) is bound to , it is negatively polarized ( ), and expected to induce the same structural change induced by CN(-). This structural change allows to receive three electron equivalents nonsequentially from , , and Tyr-OH, providing complete reduction of O(2) with minimization of production of active oxygen species. The proton-pumping pathway of bovine CcO comprises a hydrogen-bond network and a water channel which extend to the positive and negative side surfaces, respectively. Protons transferred through the water channel are pumped through the hydrogen-bond network electrostatically with positive charge created at the Fe(a) center by electron donation to the O(2) reduction site. Binding of CO or NO to induces significant narrowing of a section of the water channel near the hydrogen-bond network junction, which prevents access of water molecules to the network. In a similar manner, O(2) binding to is expected to prevent access of water molecules to the hydrogen-bond network. This blocks proton back-leak from the network and provides an efficient gate for proton-pumping.
-===Bovine Heart Cytochrome c Oxidase in the Carbon Monoxide-bound Fully Reduced State at 100 K===
+Bovine cytochrome c oxidase structures enable O2 reduction with minimization of reactive oxygens and provide a proton-pumping gate.,Muramoto K, Ohta K, Shinzawa-Itoh K, Kanda K, Taniguchi M, Nabekura H, Yamashita E, Tsukihara T, Yoshikawa S Proc Natl Acad Sci U S A. 2010 Apr 12. PMID:20385840<ref>PMID:20385840</ref>
-{{ABSTRACT_PUBMED_20385840}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 3ag2" style="background-color:#fffaf0;"></div>
-[[3ag2]] is a 26 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3AG2 OCA].
 ==See Also==
-*[[Cytochrome c oxidase|Cytochrome c oxidase]]
+*[[Cytochrome c oxidase 3D structures|Cytochrome c oxidase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:020385840</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
 [[Category: Bos taurus]]
-[[Category: Cytochrome-c oxidase]]
+[[Category: Large Structures]]
-[[Category: Kanda, K.]]
+[[Category: Kanda K]]
-[[Category: Muramoto, K.]]
+[[Category: Muramoto K]]
-[[Category: Nabekura, H.]]
+[[Category: Nabekura H]]
-[[Category: Ohta, K.]]
+[[Category: Ohta K]]
-[[Category: Shinzawa-Itoh, K.]]
+[[Category: Shinzawa-Itoh K]]
-[[Category: Taniguchi, M.]]
+[[Category: Taniguchi M]]
-[[Category: Tsukihara, T.]]
+[[Category: Tsukihara T]]
-[[Category: Yamashita, E.]]
+[[Category: Yamashita E]]
-[[Category: Yoshikawa, S.]]
+[[Category: Yoshikawa S]]
-[[Category: Electron transport]]
-[[Category: Formylation]]
-[[Category: Heme]]
-[[Category: Iron]]
-[[Category: Isopeptide bond]]
-[[Category: Membrane]]
-[[Category: Mitochondrion]]
-[[Category: Mitochondrion inner membrane]]
-[[Category: Oxidoreductase]]
-[[Category: Respiratory chain]]
-[[Category: Transit peptide]]
-[[Category: Transmembrane]]
-[[Category: Transport]]