1cpf: Difference between revisions

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OCA

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-[[Image:1cpf.jpg|left|200px]]<br /><applet load="1cpf" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="1cpf, resolution 2.2&Aring;" />
-'''A CATION BINDING MOTIF STABILIZES THE COMPOUND I RADICAL OF CYTOCHROME C PEROXIDASE'''<br />
-==Overview==
+==A CATION BINDING MOTIF STABILIZES THE COMPOUND I RADICAL OF CYTOCHROME C PEROXIDASE==
-Cytochrome c peroxidase reacts with peroxide to form compound I, which, contains an oxyferryl heme and an indolyl radical at Trp-191. The indolyl, free radical has a half-life of several hours at room temperature, and, this remarkable stability is essential for the catalytic function of, cytochrome c peroxidase. To probe the protein environment that stabilizes, the compound I radical, we used site-directed mutagenesis to replace, Trp-191 with Gly or Gln. Crystal structures of these mutants revealed a, monovalent cation binding site in the cavity formerly occupied by the side, chain of Trp-191. Comparison of this site with those found in other known, cation binding enzymes shows that the Trp-191 side chain resides in a, consensus K+ binding site. Electrostatic potential calculations indicate, that the cation binding site is created by partial negative charges at the, backbone carbonyl oxygen atoms of residues 175 and 177, the carboxyl end, of a long alpha-helix (residues 165-175), the heme propionates, and the, carboxylate side chain of Asp-235. These features create a negative, potential that envelops the side chain of Trp-191; the calculated free, energy change for cation binding in this site is -27 kcal/mol (1 cal =, 4.184J). This is more than sufficient to account for the stability of the, Trp-191 radical, which our estimates suggest is stabilized by 7.8 kcal/mol, relative to a Trp radical in solution.
+<StructureSection load='1cpf' size='340' side='right'caption='[[1cpf]], [[Resolution|resolution]] 2.20&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1cpf]] 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=1CPF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CPF 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]] 2.2&#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=TRS:2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL'>TRS</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=1cpf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cpf OCA], [https://pdbe.org/1cpf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cpf RCSB], [https://www.ebi.ac.uk/pdbsum/1cpf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cpf 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/cp/1cpf_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=1cpf ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-CPF is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Saccharomyces_cerevisiae Saccharomyces cerevisiae] with HEM and TRS as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Cytochrome-c_peroxidase Cytochrome-c peroxidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.5 1.11.1.5] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1CPF OCA].
+*[[Cytochrome c peroxidase 3D structures|Cytochrome c peroxidase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-A cation binding motif stabilizes the compound I radical of cytochrome c peroxidase., Miller MA, Han GW, Kraut J, Proc Natl Acad Sci U S A. 1994 Nov 8;91(23):11118-22. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7972020 7972020]
+[[Category: Large Structures]]
-[[Category: Cytochrome-c peroxidase]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
+[[Category: Han GW]]
-[[Category: Han, G.W.]]
+[[Category: Kraut J]]
-[[Category: Kraut, J.]]
+[[Category: Miller MA]]
-[[Category: Miller, M.A.]]
-[[Category: HEM]]
-[[Category: TRS]]
-[[Category: oxidoreductase(h2o2(a))]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 12:38:57 2007''