8ijn: Difference between revisions
New page: '''Unreleased structure''' The entry 8ijn is ON HOLD Authors: Tsukihara, T., Shimada, A., Muramoto, K. Description: Bovine Heart Cytochrome c Oxidase in the Nitric Oxide-Bound Fully Re... |
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The | ==Bovine Heart Cytochrome c Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K== | ||
<StructureSection load='8ijn' size='340' side='right'caption='[[8ijn]], [[Resolution|resolution]] 1.80Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[8ijn]] 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=8IJN OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8IJN FirstGlance]. <br> | |||
</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=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=NO:NITRIC+OXIDE'>NO</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=8ijn FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8ijn OCA], [https://pdbe.org/8ijn PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8ijn RCSB], [https://www.ebi.ac.uk/pdbsum/8ijn PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8ijn ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/COX5A_BOVIN COX5A_BOVIN] This is the heme A-containing chain of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. | |||
<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 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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: | <div class="pdbe-citations 8ijn" style="background-color:#fffaf0;"></div> | ||
[[Category: | == References == | ||
[[Category: | <references/> | ||
__TOC__ | |||
</StructureSection> | |||
[[Category: Bos taurus]] | |||
[[Category: Large Structures]] | |||
[[Category: Muramoto K]] | |||
[[Category: Shimada A]] | |||
[[Category: Tsukihara T]] | |||
Latest revision as of 23:36, 12 April 2023
Bovine Heart Cytochrome c Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 KBovine Heart Cytochrome c Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K
Structural highlights
FunctionCOX5A_BOVIN This is the heme A-containing chain of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport. Publication Abstract from PubMedThe 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 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[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References |
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