2iqf: Difference between revisions

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-[[Image:2iqf.png|left|200px]]
-{{STRUCTURE_2iqf|  PDB=2iqf  |  SCENE=  }}
+==Crystal structure of Helicobacter pylori catalase compound I==
+<StructureSection load='2iqf' size='340' side='right'caption='[[2iqf]], [[Resolution|resolution]] 1.86&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[2iqf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IQF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IQF 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]] 1.86&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=MHO:S-OXYMETHIONINE'>MHO</scene>, <scene name='pdbligand=O:OXYGEN+ATOM'>O</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=2iqf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iqf OCA], [https://pdbe.org/2iqf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2iqf RCSB], [https://www.ebi.ac.uk/pdbsum/2iqf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2iqf ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/CATA_HELPY CATA_HELPY] Decomposes hydrogen peroxide into water and oxygen; serves to protect cells from the toxic effects of hydrogen peroxide.
+== 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/iq/2iqf_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=2iqf ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The structures of Helicobacter pylori (HPC) and Penicillium vitale (PVC) catalases, each with two subunits in the crystal asymmetric unit, oxidized with peroxoacetic acid are reported at 1.8 and 1.7 A resolution, respectively. Despite the similar oxidation conditions employed, the iron-oxygen coordination length is 1.72 A for PVC, close to what is expected for a Fe=O double bond, and 1.80 and 1.85 A for HPC, suggestive of a Fe-O single bond. The structure and electronic configuration of the oxoferryl heme and immediate protein environment is investigated further by QM/MM density functional theory calculations. Four different active site electronic configurations are considered, Por*+-FeIV=O, Por*+-FeIV=O...HisH+, Por*+-FeIV-OH+ and Por-FeIV-OH (a protein radical is assumed in the latter configuration). The electronic structure of the primary oxidized species, Por*+-FeIV=O, differs qualitatively between HPC and PVC with an A2u-like porphyrin radical delocalized on the porphyrin in HPC and a mixed A1u-like "fluctuating" radical partially delocalized over the essential distal histidine, the porphyrin, and, to a lesser extent, the proximal tyrosine residue. This difference is rationalized in terms of HPC containing heme b and PVC containing heme d. It is concluded that compound I of PVC contains an oxoferryl Por*+-FeIV=O species with partial protonation of the distal histidine and compound I of HPC contains a hydroxoferryl Por-FeIV-OH with the second oxidation equivalent delocalized as a protein radical. The findings support the idea that there is a relation between radical migration to the protein and protonation of the oxoferryl bond in catalase.
-===Crystal structure of Helicobacter pylori catalase compound I===
+The structures and electronic configuration of compound I intermediates of Helicobacter pylori and Penicillium vitale catalases determined by X-ray crystallography and QM/MM density functional theory calculations.,Alfonso-Prieto M, Borovik A, Carpena X, Murshudov G, Melik-Adamyan W, Fita I, Rovira C, Loewen PC J Am Chem Soc. 2007 Apr 11;129(14):4193-205. Epub 2007 Mar 15. PMID:17358056<ref>PMID:17358056</ref>
-{{ABSTRACT_PUBMED_17358056}}
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+</div>
-==About this Structure==
+<div class="pdbe-citations 2iqf" style="background-color:#fffaf0;"></div>
-[[2iqf]] is a 2 chain structure of [[Catalase]] with sequence from [http://en.wikipedia.org/wiki/Helicobacter_pylori Helicobacter pylori]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IQF OCA].
 ==See Also==
-*[[Catalase|Catalase]]
+*[[Catalase 3D structures|Catalase 3D structures]]
+== References ==
-==Reference==
+<references/>
-<ref group="xtra">PMID:017358056</ref><references group="xtra"/>
+__TOC__
-[[Category: Catalase]]
+</StructureSection>
 [[Category: Helicobacter pylori]]
-[[Category: Carpena, X.]]
+[[Category: Large Structures]]
-[[Category: Fita, I.]]
+[[Category: Carpena X]]
-[[Category: Loewen, P C.]]
+[[Category: Fita I]]
-[[Category: Beta barrel]]
+[[Category: Loewen PC]]
-[[Category: Hydroxoferryl heme]]
-[[Category: Oxidoreductase]]