3om3: Difference between revisions

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-[[Image:3om3.png|left|200px]]
-<!--
+==Catalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides with K362M mutation in the reduced state==
-The line below this paragraph, containing "STRUCTURE_3om3", creates the "Structure Box" on the page.
+<StructureSection load='3om3' size='340' side='right'caption='[[3om3]], [[Resolution|resolution]] 2.60&Aring;' scene=''>
-You may change the PDB parameter (which sets the PDB file loaded into the applet)
+== Structural highlights ==
-or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+<table><tr><td colspan='2'>[[3om3]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Cereibacter_sphaeroides_2.4.1 Cereibacter sphaeroides 2.4.1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OM3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3OM3 FirstGlance]. <br>
-or leave the SCENE parameter empty for the default display.
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CD:CADMIUM+ION'>CD</scene>, <scene name='pdbligand=CU1:COPPER+(I)+ION'>CU1</scene>, <scene name='pdbligand=DMU:DECYL-BETA-D-MALTOPYRANOSIDE'>DMU</scene>, <scene name='pdbligand=HEA:HEME-A'>HEA</scene>, <scene name='pdbligand=HTH:(2S,3R)-HEPTANE-1,2,3-TRIOL'>HTH</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=TRD:TRIDECANE'>TRD</scene></td></tr>
-{{STRUCTURE_3om3|  PDB=3om3  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=3om3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3om3 OCA], [https://pdbe.org/3om3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3om3 RCSB], [https://www.ebi.ac.uk/pdbsum/3om3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3om3 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/Q3J5A7_CERS4 Q3J5A7_CERS4] 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.[RuleBase:RU363061]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Crystal structures in both oxidized and reduced forms are reported for two bacterial cytochrome c oxidase mutants that define the D and K proton paths, showing conformational change in response to reduction and the loss of strategic waters that can account for inhibition of proton transfer. In the oxidized state both mutants of the Rhodobacter sphaeroides enzyme, D132A and K362M, show overall structures similar to wild type, indicating no long-range effects of mutation. In the reduced state, the mutants show an altered conformation similar to that seen in reduced wild type, confirming this reproducible, reversible response to reduction. In the strongly inhibited D132A mutant, positions of residues and waters in the D pathway are unaffected except in the entry region close to the mutation, where a chloride ion replaces the missing carboxyl and a 2-A shift in N207 results in loss of its associated water. In K362M, the methionine occupies the same position as the original lysine, but K362- and T359-associated waters in the wild-type structure are missing, likely accounting for the severe inhibition. Spectra of oxidized frozen crystals taken during X-ray radiation show metal center reduction, but indicate development of a strained configuration that only relaxes to a native form upon annealing. Resistance of the frozen crystal to structural change clarifies why the oxidized conformation is observable and supports the conclusion that the reduced conformation has functional significance. A mechanism is described that explains the conformational change and the incomplete response of the D-path mutant.
-===Catalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides with K362M mutation in the reduced state===
+Crystallographic and online spectral evidence for role of conformational change and conserved water in cytochrome oxidase proton pump.,Liu J, Qin L, Ferguson-Miller S Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1284-9. Epub 2011 Jan 4. PMID:21205904<ref>PMID:21205904</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 3om3" style="background-color:#fffaf0;"></div>
-<!--
+==See Also==
-The line below this paragraph, {{ABSTRACT_PUBMED_21205904}}, adds the Publication Abstract to the page
+*[[Cytochrome c oxidase 3D structures|Cytochrome c oxidase 3D structures]]
-(as it appears on PubMed at http://www.pubmed.gov), where 21205904 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_21205904}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Cereibacter sphaeroides 2 4.1]]
-[[3om3]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides_2.4.1 Rhodobacter sphaeroides 2.4.1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3OM3 OCA].
+[[Category: Large Structures]]
+[[Category: Ferguson-Miller S]]
-==Reference==
+[[Category: Liu J]]
-<ref group="xtra">PMID:21205904</ref><references group="xtra"/>
+[[Category: Qin L]]
-[[Category: Oxidoreductase]]
-[[Category: Rhodobacter sphaeroides 2 4.1]]
-[[Category: Ferguson-Miller, S.]]
-[[Category: Liu, J.]]
-[[Category: Qin, L.]]