2xil: Difference between revisions

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-{{Seed}}
-[[Image:2xil.jpg|left|200px]]
-<!--
+==The structure of cytochrome c peroxidase Compound I==
-The line below this paragraph, containing "STRUCTURE_2xil", creates the "Structure Box" on the page.
+<StructureSection load='2xil' size='340' side='right'caption='[[2xil]], [[Resolution|resolution]] 1.68&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'>[[2xil]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XIL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2XIL 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]] 1.68&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=MRD:(4R)-2-METHYLPENTANE-2,4-DIOL'>MRD</scene>, <scene name='pdbligand=PO4:PHOSPHATE+ION'>PO4</scene></td></tr>
-{{STRUCTURE_2xil|  PDB=2xil  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2xil FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2xil OCA], [https://pdbe.org/2xil PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2xil RCSB], [https://www.ebi.ac.uk/pdbsum/2xil PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2xil ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CCPR_YEAST CCPR_YEAST] Destroys radicals which are normally produced within the cells and which are toxic to biological systems.
+== 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/xi/2xil_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=2xil ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Heme enzymes are ubiquitous in biology and catalyse a vast array of biological redox processes. The formation of high-valent ferryl intermediates of the heme iron (known as Compounds I and Compound II) is implicated for number of catalytic heme enzymes, but these species are formed only transiently and thus have proved somewhat elusive. In consequence, there has been conflicting evidence as to the nature of these ferryl intermediates in a number of different heme enzymes, in particular the precise nature of the bond between the heme iron and the bound oxygen atom. In this work, we present high-resolution crystal structures of both Compound I and Compound II intermediates in two different heme peroxidase enzymes, cytochrome c peroxidase and ascorbate peroxidase, allowing direct and accurate comparison of the bonding interactions in the different intermediates. A consistent picture emerges across all structures, showing lengthening of the ferryl oxygen bond (and presumed protonation) on reduction of Compound I to Compound II. These data clarify long-standing inconsistencies on the nature of the ferryl heme species in these intermediates.
-===THE NATURE OF THE FERRYL HEME SPECIES IN COMPOUNDS I AND II===
+The nature of the ferryl heme in compounds I and II.,Gumiero A, Metcalfe CL, Pearson AR, Raven EL, Moody PC J Biol Chem. 2010 Nov 8. PMID:21062738<ref>PMID:21062738</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
+<div class="pdbe-citations 2xil" style="background-color:#fffaf0;"></div>
-==About this Structure==
+==See Also==
-XIL is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2XIL OCA].
+*[[Cytochrome c peroxidase 3D structures|Cytochrome c peroxidase 3D structures]]
-[[Category: Cytochrome-c peroxidase]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Large Structures]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Gumiero, A.]]
+[[Category: Gumiero A]]
-[[Category: Moody, P C.E.]]
+[[Category: Moody PCE]]
-[[Category: Raven, E L.]]
+[[Category: Raven EL]]
-[[Category: Apx]]
-[[Category: Ascorbate peroxidase]]
-[[Category: Compound iii]]
-[[Category: Ferrous heme]]
-[[Category: Ferryl ion]]
-[[Category: Oxidoreductase]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Jul 14 16:17:16 2010''