5xdx: Difference between revisions
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New page: '''Unreleased structure''' The entry 5xdx is ON HOLD Authors: Luo, F.J, Shimada, A, Hagimoto, N, Shimada, S, Shinzawa-Itoh, K, Yamashita, E, Yoshikawa, S, Tsukihara, T Description: Bov... |
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The | ==Bovine heart cytochrome c oxidase in the reduced state with pH 7.3 at 1.99 angstrom resolution== | ||
<StructureSection load='5xdx' size='340' side='right'caption='[[5xdx]], [[Resolution|resolution]] 1.99Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[5xdx]] 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=5XDX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5XDX 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]] 1.99Å</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=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=5xdx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5xdx OCA], [https://pdbe.org/5xdx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5xdx RCSB], [https://www.ebi.ac.uk/pdbsum/5xdx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5xdx ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/COX2_BOVIN COX2_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. Subunit 2 transfers the electrons from cytochrome c via its binuclear copper A center to the bimetallic center of the catalytic subunit 1. | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
Cytochrome c oxidase (CcO), the terminal oxidase in cellular respiration, couples proton pumping to O2 reduction. Mammalian CcO resides in the inner mitochondrial membrane. Previously, a model of H-pathway proton pumping was proposed based on various CcO crystal structures. However, all previously determined structures were solved using crystals obtained at pH 5.7, which differs from the environmental pH of CcO in the inner membrane. The structures of fully oxidized and ligand-free reduced CcO at pH 7.3 have now been determined. Structural comparison between the oxidized and reduced states revealed that the structural alterations that occurred upon redox change at pH 5.7 in Asp51, the magnesium-containing cluster, haem groups and helix X, which provide important structural evidence for the H-pathway proton-pumping proposal, also occur at pH 7.3. These structural alterations were restricted to a local region of CcO; no domain movement was detected, nor were significant structural alterations detected in peripheral regions at either pH value. These observations indicate that the small and precise structural alterations that occur over the course of the reaction cycle are not affected by pH change, and that isolated CcO precisely performs proton pumping via the H-pathway over a wide pH range. Because the pH is not uniform across the molecular surface of CcO, the fact that the overall structure of CcO is not affected by pH changes ensures the high enzymatic efficiency of this protein in the mitochondria. | |||
Structure of bovine cytochrome c oxidase in the ligand-free reduced state at neutral pH.,Luo F, Shinzawa-Itoh K, Hagimoto K, Shimada A, Shimada S, Yamashita E, Yoshikawa S, Tsukihara T Acta Crystallogr F Struct Biol Commun. 2018 Feb 1;74(Pt 2):92-98. doi:, 10.1107/S2053230X17018532. Epub 2018 Jan 26. PMID:29400318<ref>PMID:29400318</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
[[Category: Luo | <div class="pdbe-citations 5xdx" style="background-color:#fffaf0;"></div> | ||
==See Also== | |||
*[[Cytochrome c oxidase 3D structures|Cytochrome c oxidase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Bos taurus]] | |||
[[Category: Large Structures]] | |||
[[Category: Hagimoto N]] | |||
[[Category: Luo FJ]] | |||
[[Category: Shimada A]] | |||
[[Category: Shimada S]] | |||
[[Category: Shinzawa-Itoh K]] | |||
[[Category: Tsukihara T]] | |||
[[Category: Yamashita E]] | |||
[[Category: Yoshikawa S]] | |||
