8gvm: Difference between revisions

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-'''Unreleased structure'''
-The entry 8gvm is ON HOLD
+==The structure of azide-bound cytochrome C oxidase determined using the crystals exposed to 20 mm azide solution for 4 days==
+<StructureSection load='8gvm' size='340' side='right'caption='[[8gvm]], [[Resolution|resolution]] 1.85&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8gvm]] 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=8GVM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8GVM 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]] 1.851&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <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=8gvm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8gvm OCA], [https://pdbe.org/8gvm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8gvm RCSB], [https://www.ebi.ac.uk/pdbsum/8gvm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8gvm ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/COX7B_BOVIN COX7B_BOVIN] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Cytochrome c oxidase (CcO) is the terminal oxidase of cellular respiration, reducing O2 to water and pumping protons. X-ray structural features have suggested that CcO pumps protons via a mechanism involving electrostatic repulsions between pumping protons in the hydrogen bond network of a proton-conducting pathway (the H-pathway) and net positive charges created upon oxidation of an iron site, heme alpha (Fe alpha(2+)), for reduction of O2 at another iron site, heme alpha3 (Fe alpha3(2+)). The protons for pumping are transferred to the hydrogen bond network from the N-side via the water channel of the H-pathway. Back-leakage of protons to the N-side is thought to be blocked by closure of the water channel. To experimentally test this, we examined X-ray structures of the azide-bound, oxidized bovine CcO and found that an azide derivative (N3(-)-Fe alpha3(3+), CuB(2+)-N3(-)) induces a translational movement of the heme alpha3 plane. This was accompanied by opening of the water channel, revealing that Fe alpha3 and the H-pathway are tightly coupled. The channel opening in the oxidized state is likely to induce back-leakage of pumping protons which lowers the proton level in the hydrogen bond network during enzymatic turnover. The proton level decrease weakens the electron affinity of Fe alpha , if Fe alpha electrostatically interacts with protons in the hydrogen bond network. The previously reported azide-induced redox-potential decrease in Fe alpha supports existence of the electrostatic interaction. In summary, our results indicate that the H-pathway is critical for CcO's proton-pumping function.
-Authors: Tsukihara, T., Shimada, A.
+X-ray structural analyses of azide-bound cytochrome c oxidases reveal that the H-pathway is critically important for the proton-pumping activity.,Shimada A, Hatano K, Tadehara H, Yano N, Shinzawa-Itoh K, Yamashita E, Muramoto K, Tsukihara T, Yoshikawa S J Biol Chem. 2018 Aug 3. pii: RA118.003123. doi: 10.1074/jbc.RA118.003123. PMID:30077971<ref>PMID:30077971</ref>
-Description: THE STRUCTURE OF AZIDE-BOUND CYTOCHROME C OXIDASE DETERMINED USING THE CRYSTALS EXPOSED TO 20 MM AZIDE SOLUTION FOR 4 DAYS
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Shimada, A]]
+<div class="pdbe-citations 8gvm" style="background-color:#fffaf0;"></div>
-[[Category: Tsukihara, T]]
+==See Also==
+*[[Cytochrome c oxidase 3D structures|Cytochrome c oxidase 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Bos taurus]]
+[[Category: Large Structures]]
+[[Category: Shimada A]]
+[[Category: Tsukihara T]]