1ml2: Difference between revisions

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-[[Image:1ml2.gif|left|200px]]<br /><applet load="1ml2" size="350" color="white" frame="true" align="right" spinBox="true"
-caption="1ml2, resolution 1.65&Aring;" />
-'''Crystal Structure of a Mutant Variant of Cytochrome c Peroxidase with Zn(II)-(20-oxo-Protoporphyrin IX)'''<br />
-==Overview==
+==Crystal Structure of a Mutant Variant of Cytochrome c Peroxidase with Zn(II)-(20-oxo-Protoporphyrin IX)==
-The crystal structure of a cytochrome c peroxidase mutant where the distal catalytic His52 is converted to Tyr reveals that the tyrosine side-chain forms a covalent bond with the indole ring nitrogen atom of Trp51. We hypothesize that this novel bond results from peroxide activation by the heme iron followed by oxidation of Trp51 and Tyr52. This hypothesis has been tested by incorporation of a redox-inactive Zn-protoporphyrin into the protein, and the resulting crystal structure shows the absence of a Trp51-Tyr52 cross-link. Instead, the Tyr52 side-chain orients away from the heme active-site pocket, which requires a substantial rearrangement of residues 72-80 and 134-144. Additional experiments where heme-containing crystals of the mutant were treated with peroxide support our hypothesis that this novel Trp-Tyr cross-link is a peroxide-dependent process mediated by the heme iron.
+<StructureSection load='1ml2' size='340' side='right'caption='[[1ml2]], [[Resolution|resolution]] 1.65&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1ml2]] 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=1ML2 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ML2 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]] 1.65&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ZEM:20-OXO-PROTOPORPHYRIN+IX+CONTAINING+ZN(II)'>ZEM</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=1ml2 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ml2 OCA], [https://pdbe.org/1ml2 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ml2 RCSB], [https://www.ebi.ac.uk/pdbsum/1ml2 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ml2 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/ml/1ml2_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=1ml2 ConSurf].
+<div style="clear:both"></div>
-==About this Structure==
+==See Also==
-ML2 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 <scene name='pdbligand=ZEM:'>ZEM</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. 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://oca.weizmann.ac.il/oca-bin/ocashort?id=1ML2 OCA].
+*[[Cytochrome c peroxidase 3D structures|Cytochrome c peroxidase 3D structures]]
+__TOC__
-==Reference==
+</StructureSection>
-A novel heme and peroxide-dependent tryptophan-tyrosine cross-link in a mutant of cytochrome c peroxidase., Bhaskar B, Immoos CE, Shimizu H, Sulc F, Farmer PJ, Poulos TL, J Mol Biol. 2003 Apr 18;328(1):157-66. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12684005 12684005]
+[[Category: Large Structures]]
-[[Category: Cytochrome-c peroxidase]]
 [[Category: Saccharomyces cerevisiae]]
-[[Category: Single protein]]
+[[Category: Bhaskar B]]
-[[Category: Bhaskar, B.]]
+[[Category: Farmer PJ]]
-[[Category: Farmer, P J.]]
+[[Category: Immoos CE]]
-[[Category: Immoos, C E.]]
+[[Category: Poulos TL]]
-[[Category: Poulos, T L.]]
+[[Category: Shimizu H]]
-[[Category: Shimizu, H.]]
-[[Category: ZEM]]
-[[Category: cytochrome c peroxidase]]
-[[Category: oxygen radical]]
-[[Category: trp cation radical]]
-[[Category: trp-tyr covalent cross-link]]
-[[Category: zn-protoporphyrin ix]]
-[[Category: znccp]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:56:16 2008''