1qwl: Difference between revisions

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-[[Image:1qwl.gif|left|200px]]
-<!--
+==Structure of Helicobacter pylori catalase==
-The line below this paragraph, containing "STRUCTURE_1qwl", creates the "Structure Box" on the page.
+<StructureSection load='1qwl' size='340' side='right'caption='[[1qwl]], [[Resolution|resolution]] 1.60&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'>[[1qwl]] 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=1QWL OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1QWL 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]] 1.6&#8491;</td></tr>
--->
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=OXY:OXYGEN+MOLECULE'>OXY</scene></td></tr>
-{{STRUCTURE_1qwl|  PDB=1qwl  |  SCENE=  }}
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1qwl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qwl OCA], [https://pdbe.org/1qwl PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1qwl RCSB], [https://www.ebi.ac.uk/pdbsum/1qwl PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1qwl 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/qw/1qwl_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=1qwl ConSurf].
+<div style="clear:both"></div>
-'''Structure of Helicobacter pylori catalase'''
+==See Also==
+*[[Catalase 3D structures|Catalase 3D structures]]
+__TOC__
-==Overview==
+</StructureSection>
-Helicobacter pylori produces one monofunctional catalase, encoded by katA (hp0875). The crystal structure of H. pylori catalase (HPC) has been determined and refined at 1.6 A with crystallographic agreement factors R and R(free) of 17.4 and 21.9%, respectively. The crystal exhibits P2(1)2(1)2 space group symmetry and contains two protein subunits in the asymmetric unit. The core structure of the HPC subunit, including the disposition of a heme b prosthetic group, is closely related to those of other catalases, although it appears to be the only clade III catalase that has been characterized that does not bind NADPH. The heme iron in one subunit of the native enzyme appears to be covalently modified, possibly with a perhydroxy or dioxygen group in a compound III-like structure. Formic acid is known to bind in the active site of catalases, promoting the breakdown of reaction intermediates compound I and compound II. The structure of an HPC crystal soaked with sodium formate at pH 5.6 has also been determined to 1.6 A (with R and R(free) values of 18.1 and 20.7%, respectively), revealing at least 36 separate formate or formic acid residues in the HPC dimer. In turn, the number of water molecules refined into the models decreased from 1016 in the native enzyme to 938 in the formate-treated enzyme. Extra density, interpreted as azide, is found in a location of both structures that involves interaction with all four subunits in the tetramer. Electron paramagnetic resonance spectra confirm that azide does not bind as a ligand of the iron and that formate does bind in the heme pocket. The stability of the formate or formic acid molecule found inside the heme distal pocket has been investigated by calculations based on density functional theory.
-==About this Structure==
-QWL is a [[Single protein]] structure of 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=1QWL OCA].
-==Reference==
-Structure of Helicobacter pylori catalase, with and without formic acid bound, at 1.6 A resolution., Loewen PC, Carpena X, Rovira C, Ivancich A, Perez-Luque R, Haas R, Odenbreit S, Nicholls P, Fita I, Biochemistry. 2004 Mar 23;43(11):3089-103. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/15023060 15023060]
-[[Category: Catalase]]
 [[Category: Helicobacter pylori]]
-[[Category: Single protein]]
+[[Category: Large Structures]]
-[[Category: Carpena, X.]]
+[[Category: Carpena X]]
-[[Category: Fita, I.]]
+[[Category: Fita I]]
-[[Category: Haas, R.]]
+[[Category: Haas R]]
-[[Category: Loewen, P C.]]
+[[Category: Loewen PC]]
-[[Category: Nicholls, P.]]
+[[Category: Nicholls P]]
-[[Category: Obenbreit, S.]]
+[[Category: Obenbreit S]]
-[[Category: Perez-Luque, R.]]
+[[Category: Perez-Luque R]]
-[[Category: Rovira, C.]]
+[[Category: Rovira C]]
-[[Category: Azide complex]]
-[[Category: Beta barrel]]
-[[Category: Oxyferryl complex]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May  3 06:46:58 2008''