2gsm: Difference between revisions

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-[[Image:2gsm.png|left|200px]]
-{{STRUCTURE_2gsm|  PDB=2gsm  |  SCENE=  }}
+==Catalytic Core (Subunits I and II) of Cytochrome c oxidase from Rhodobacter sphaeroides==
+<StructureSection load='2gsm' size='340' side='right'caption='[[2gsm]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2gsm]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/"rhodococcus_capsulatus"_molisch_1907 "rhodococcus capsulatus" molisch 1907]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GSM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2GSM FirstGlance]. <br>
+</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=CU:COPPER+(II)+ION'>CU</scene>, <scene name='pdbligand=DMU:DECYL-BETA-D-MALTOPYRANOSIDE'>DMU</scene>, <scene name='pdbligand=HEA:HEME-A'>HEA</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OH:HYDROXIDE+ION'>OH</scene>, <scene name='pdbligand=TRD:TRIDECANE'>TRD</scene></td></tr>
+<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">ctaD ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1063 "Rhodococcus capsulatus" Molisch 1907]), ctaC, coxII, ctaB ([https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=1063 "Rhodococcus capsulatus" Molisch 1907])</td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Cytochrome-c_oxidase Cytochrome-c oxidase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.9.3.1 1.9.3.1] </span></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=2gsm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2gsm OCA], [https://pdbe.org/2gsm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2gsm RCSB], [https://www.ebi.ac.uk/pdbsum/2gsm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2gsm ProSAT]</span></td></tr>
+</table>
+== Function ==
+[[https://www.uniprot.org/uniprot/COX1_RHOSH COX1_RHOSH]] 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. This cytochrome c oxidase shows proton pump activity across the membrane in addition to the electron transfer. [[https://www.uniprot.org/uniprot/COX2_RHOSH COX2_RHOSH]] Subunits I and II form the functional core of the enzyme complex. Electrons originating in cytochrome c are transferred via heme a and Cu(A) to the binuclear center formed by heme a3 and Cu(B).
+== 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/gs/2gsm_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=2gsm ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Well ordered reproducible crystals of cytochrome c oxidase (CcO) from Rhodobacter sphaeroides yield a previously unreported structure at 2.0 A resolution that contains the two catalytic subunits and a number of alkyl chains of lipids and detergents. Comparison with crystal structures of other bacterial and mammalian CcOs reveals that the positions occupied by native membrane lipids and detergent substitutes are highly conserved, along with amino acid residues in their vicinity, suggesting a more prevalent and specific role of lipid in membrane protein structure than often envisioned. Well defined detergent head groups (maltose) are found associated with aromatic residues in a manner similar to phospholipid head groups, likely contributing to the success of alkyl glycoside detergents in supporting membrane protein activity and crystallizability. Other significant features of this structure include the following: finding of a previously unreported crystal contact mediated by cadmium and an engineered histidine tag; documentation of the unique His-Tyr covalent linkage close to the active site; remarkable conservation of a chain of waters in one proton pathway (D-path); and discovery of an inhibitory cadmium-binding site at the entrance to another proton path (K-path). These observations provide important insight into CcO structure and mechanism, as well as the significance of bound lipid in membrane proteins.
-===Catalytic Core (Subunits I and II) of Cytochrome c oxidase from Rhodobacter sphaeroides===
+Identification of conserved lipid/detergent-binding sites in a high-resolution structure of the membrane protein cytochrome c oxidase.,Qin L, Hiser C, Mulichak A, Garavito RM, Ferguson-Miller S Proc Natl Acad Sci U S A. 2006 Oct 31;103(44):16117-22. Epub 2006 Oct 18. PMID:17050688<ref>PMID:17050688</ref>
-{{ABSTRACT_PUBMED_17050688}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2gsm" style="background-color:#fffaf0;"></div>
-[[2gsm]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Rhodobacter_sphaeroides Rhodobacter sphaeroides]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2GSM OCA].
 ==See Also==
-*[[Cytochrome c oxidase|Cytochrome c oxidase]]
+*[[Cytochrome c oxidase 3D structures|Cytochrome c oxidase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:017050688</ref><references group="xtra"/>
+__TOC__
+</StructureSection>
+[[Category: Rhodococcus capsulatus molisch 1907]]
 [[Category: Cytochrome-c oxidase]]
-[[Category: Rhodobacter sphaeroides]]
+[[Category: Large Structures]]
-[[Category: Ferguson-Miller, S.]]
+[[Category: Ferguson-Miller, S]]
-[[Category: Garavito, R M.]]
+[[Category: Garavito, R M]]
-[[Category: Hiser, C.]]
+[[Category: Hiser, C]]
-[[Category: Mulichak, A.]]
+[[Category: Mulichak, A]]
-[[Category: Qin, L.]]
+[[Category: Qin, L]]
 [[Category: Oxidoreductase]]
 [[Category: Transmembrane protein complex]]