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== | ==The structures of Penicillium vitale catalase: resting state, oxidised state (compound I) and complex with aminotriazole== | ||
<StructureSection load='2iuf' size='340' side='right'caption='[[2iuf]], [[Resolution|resolution]] 1.71Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[2iuf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Penicillium_janthinellum Penicillium janthinellum]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2IUF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2IUF FirstGlance]. <br> | |||
</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=F50:ETHANEPEROXOIC+ACID'>F50</scene>, <scene name='pdbligand=HDD:CIS-HEME+D+HYDROXYCHLORIN+GAMMA-SPIROLACTONE'>HDD</scene>, <scene name='pdbligand=MPD:(4S)-2-METHYL-2,4-PENTANEDIOL'>MPD</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</scene>, <scene name='pdbligand=O:OXYGEN+ATOM'>O</scene></td></tr> | |||
<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=MHO:S-OXYMETHIONINE'>MHO</scene></td></tr> | |||
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[https://en.wikipedia.org/wiki/Catalase Catalase], with EC number [https://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6] </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=2iuf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2iuf OCA], [https://pdbe.org/2iuf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2iuf RCSB], [https://www.ebi.ac.uk/pdbsum/2iuf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2iuf ProSAT]</span></td></tr> | |||
</table> | |||
== 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/iu/2iuf_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=2iuf 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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
<div class="pdbe-citations 2iuf" style="background-color:#fffaf0;"></div> | |||
==See Also== | |||
*[[Catalase 3D structures|Catalase 3D structures]] | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Catalase]] | [[Category: Catalase]] | ||
[[Category: Large Structures]] | |||
[[Category: Penicillium janthinellum]] | [[Category: Penicillium janthinellum]] | ||
[[Category: Barynin, V]] | |||
[[Category: Barynin, V | [[Category: Borovik, A]] | ||
[[Category: Borovik, A | [[Category: Grebenko, A]] | ||
[[Category: Grebenko, A | [[Category: Melik-Adamyan, W]] | ||
[[Category: Melik-Adamyan, W | [[Category: Murshudov, G]] | ||
[[Category: Murshudov, G | [[Category: Vagin, A]] | ||
[[Category: Vagin, A | [[Category: Oxidoreductase]] | ||
[[Category: | |||