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==Structure of Helicobacter pylori catalase==
==Structure of Helicobacter pylori catalase==
<StructureSection load='1qwl' size='340' side='right' caption='[[1qwl]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
<StructureSection load='1qwl' size='340' side='right'caption='[[1qwl]], [[Resolution|resolution]] 1.60&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
<table><tr><td colspan='2'>[[1qwl]] is a 2 chain structure 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=1QWL OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1QWL FirstGlance]. <br>
<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>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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>
</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='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1qwm|1qwm]]</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>
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">katA (hp0875) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 Helicobacter pylori])</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=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>
<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catalase Catalase], with EC number [http://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'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1qwl FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1qwl OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1qwl RCSB], [http://www.ebi.ac.uk/pdbsum/1qwl PDBsum]</span></td></tr>
</table>
</table>
== Function ==
== Function ==
[[http://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.  
[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 ==
== Evolutionary Conservation ==
[[Image:Consurf_key_small.gif|200px|right]]
[[Image:Consurf_key_small.gif|200px|right]]
Check<jmol>
Check<jmol>
   <jmolCheckbox>
   <jmolCheckbox>
     <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/qw/1qwl_consurf.spt"</scriptWhenChecked>
     <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>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
   </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/chain_selection.php?pdb_ID=2ata ConSurf].
</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>
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
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.
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:15023060<ref>PMID:15023060</ref>
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>


==See Also==
==See Also==
*[[Catalase|Catalase]]
*[[Catalase 3D structures|Catalase 3D structures]]
== References ==
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
[[Category: Catalase]]
[[Category: Helicobacter pylori]]
[[Category: Helicobacter pylori]]
[[Category: Carpena, X]]
[[Category: Large Structures]]
[[Category: Fita, I]]
[[Category: Carpena X]]
[[Category: Haas, R]]
[[Category: Fita I]]
[[Category: Loewen, P C]]
[[Category: Haas R]]
[[Category: Nicholls, P]]
[[Category: Loewen PC]]
[[Category: Obenbreit, S]]
[[Category: Nicholls P]]
[[Category: Perez-Luque, R]]
[[Category: Obenbreit S]]
[[Category: Rovira, C]]
[[Category: Perez-Luque R]]
[[Category: Azide complex]]
[[Category: Rovira C]]
[[Category: Beta barrel]]
[[Category: Oxidoreductase]]
[[Category: Oxyferryl complex]]

Latest revision as of 11:18, 14 February 2024

Structure of Helicobacter pylori catalaseStructure of Helicobacter pylori catalase

Structural highlights

1qwl is a 2 chain structure with sequence from Helicobacter pylori. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:X-ray diffraction, Resolution 1.6Å
Ligands:, ,
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

CATA_HELPY Decomposes hydrogen peroxide into water and oxygen; serves to protect cells from the toxic effects of hydrogen peroxide.

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

See Also

1qwl, resolution 1.60Å

Drag the structure with the mouse to rotate

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