1v54: Difference between revisions

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'''Bovine heart cytochrome c oxidase at the fully oxidized state'''<br />


==Overview==
==Bovine heart cytochrome c oxidase at the fully oxidized state==
Mitochondrial cytochrome c oxidase plays an essential role in aerobic, cellular respiration, reducing dioxygen to water in a process coupled with, the pumping of protons across the mitochondrial inner membrane. An, aspartate residue, Asp-51, located near the enzyme surface, undergoes a, redox-coupled x-ray structural change, which is suggestive of a role for, this residue in redox-driven proton pumping. However, functional or, mechanistic evidence for the involvement of this residue in proton pumping, has not yet been obtained. We report that the Asp-51 --&gt; Asn mutation of, the bovine enzyme abolishes its proton-pumping function without impairment, of the dioxygen reduction activity. Improved x-ray structures (at, 1.8/1.9-A resolution in the fully oxidized/reduced states) show that the, net positive charge created upon oxidation of the low-spin heme of the, enzyme drives the active proton transport from the interior of the, mitochondria to Asp-51 across the enzyme via a water channel and a, hydrogen-bond network, located in tandem, and that the enzyme reduction, induces proton ejection from the aspartate to the mitochondrial exterior., A peptide bond in the hydrogen-bond network critically inhibits reverse, proton transfer through the network. A redox-coupled change in the, capacity of the water channel, induced by the hydroxyfarnesylethyl group, of the low-spin heme, suggests that the channel functions as an effective, proton-collecting region. Infrared results indicate that the conformation, of Asp-51 is controlled only by the oxidation state of the low-spin heme., These results indicate that the low-spin heme drives the proton-pumping, process.
<StructureSection load='1v54' size='340' side='right'caption='[[1v54]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1v54]] 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=1V54 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1V54 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]] 1.8&#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=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=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=UNX:UNKNOWN+ATOM+OR+ION'>UNX</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=1v54 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1v54 OCA], [https://pdbe.org/1v54 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1v54 RCSB], [https://www.ebi.ac.uk/pdbsum/1v54 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1v54 ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/CX6A2_BOVIN CX6A2_BOVIN] This protein is one of the nuclear-coded polypeptide chains of cytochrome c oxidase, the terminal oxidase in mitochondrial electron transport.
== 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/v5/1v54_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=1v54 ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Mitochondrial cytochrome c oxidase plays an essential role in aerobic cellular respiration, reducing dioxygen to water in a process coupled with the pumping of protons across the mitochondrial inner membrane. An aspartate residue, Asp-51, located near the enzyme surface, undergoes a redox-coupled x-ray structural change, which is suggestive of a role for this residue in redox-driven proton pumping. However, functional or mechanistic evidence for the involvement of this residue in proton pumping has not yet been obtained. We report that the Asp-51 --&gt; Asn mutation of the bovine enzyme abolishes its proton-pumping function without impairment of the dioxygen reduction activity. Improved x-ray structures (at 1.8/1.9-A resolution in the fully oxidized/reduced states) show that the net positive charge created upon oxidation of the low-spin heme of the enzyme drives the active proton transport from the interior of the mitochondria to Asp-51 across the enzyme via a water channel and a hydrogen-bond network, located in tandem, and that the enzyme reduction induces proton ejection from the aspartate to the mitochondrial exterior. A peptide bond in the hydrogen-bond network critically inhibits reverse proton transfer through the network. A redox-coupled change in the capacity of the water channel, induced by the hydroxyfarnesylethyl group of the low-spin heme, suggests that the channel functions as an effective proton-collecting region. Infrared results indicate that the conformation of Asp-51 is controlled only by the oxidation state of the low-spin heme. These results indicate that the low-spin heme drives the proton-pumping process.


==About this Structure==
The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process.,Tsukihara T, Shimokata K, Katayama Y, Shimada H, Muramoto K, Aoyama H, Mochizuki M, Shinzawa-Itoh K, Yamashita E, Yao M, Ishimura Y, Yoshikawa S Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15304-9. Epub 2003 Dec 12. PMID:14673090<ref>PMID:14673090</ref>
1V54 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus] with DMU, CU, MG, NA, ZN, HEA, CHD, CDL, TGL, PSC, PEK, PGV, CUA and UNX as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1V54 OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
The low-spin heme of cytochrome c oxidase as the driving element of the proton-pumping process., Tsukihara T, Shimokata K, Katayama Y, Shimada H, Muramoto K, Aoyama H, Mochizuki M, Shinzawa-Itoh K, Yamashita E, Yao M, Ishimura Y, Yoshikawa S, Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15304-9. Epub 2003 Dec 12. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=14673090 14673090]
</div>
<div class="pdbe-citations 1v54" 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: Bos taurus]]
[[Category: Cytochrome-c oxidase]]
[[Category: Large Structures]]
[[Category: Protein complex]]
[[Category: Aoyama H]]
[[Category: Aoyama, H.]]
[[Category: Ishimura Y]]
[[Category: Ishimura, Y.]]
[[Category: Katayama Y]]
[[Category: Katayama, Y.]]
[[Category: Mochizuki M]]
[[Category: Mochizuki, M.]]
[[Category: Muramoto K]]
[[Category: Muramoto, K.]]
[[Category: Shimada H]]
[[Category: Shimada, H.]]
[[Category: Shimokata K]]
[[Category: Shimokata, K.]]
[[Category: Shinzawa-Itoh K]]
[[Category: Shinzawa-Itoh, K.]]
[[Category: Tsukihara T]]
[[Category: Tsukihara, T.]]
[[Category: Yamashita E]]
[[Category: Yamashita, E.]]
[[Category: Yao M]]
[[Category: Yao, M.]]
[[Category: Yoshikawa S]]
[[Category: Yoshikawa, S.]]
[[Category: CDL]]
[[Category: CHD]]
[[Category: CU]]
[[Category: CUA]]
[[Category: DMU]]
[[Category: HEA]]
[[Category: MG]]
[[Category: NA]]
[[Category: PEK]]
[[Category: PGV]]
[[Category: PSC]]
[[Category: TGL]]
[[Category: UNX]]
[[Category: ZN]]
[[Category: oxidoreductase]]
 
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