1qwl: Difference between revisions
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
[[Image:1qwl.gif|left|200px]] | [[Image:1qwl.gif|left|200px]] | ||
'''Structure of Helicobacter pylori catalase''' | {{Structure | ||
|PDB= 1qwl |SIZE=350|CAPTION= <scene name='initialview01'>1qwl</scene>, resolution 1.60Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=AZI:AZIDE+ION'>AZI</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene> and <scene name='pdbligand=OXY:OXYGEN MOLECULE'>OXY</scene> | |||
|ACTIVITY= [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] | |||
|GENE= katA (hp0875) ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=210 Helicobacter pylori]) | |||
}} | |||
'''Structure of Helicobacter pylori catalase''' | |||
==Overview== | ==Overview== | ||
| Line 7: | Line 16: | ||
==About this Structure== | ==About this Structure== | ||
1QWL is a [ | 1QWL 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== | ==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:// | 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: Catalase]] | ||
[[Category: Helicobacter pylori]] | [[Category: Helicobacter pylori]] | ||
| Line 29: | Line 38: | ||
[[Category: oxyferryl complex]] | [[Category: oxyferryl complex]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 13:43:40 2008'' | ||
Revision as of 14:43, 20 March 2008
| |||||||
| , resolution 1.60Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , and | ||||||
| Gene: | katA (hp0875) (Helicobacter pylori) | ||||||
| Activity: | Catalase, with EC number 1.11.1.6 | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
Structure of Helicobacter pylori catalase
OverviewOverview
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 StructureAbout this Structure
1QWL is a Single protein structure of sequence from Helicobacter pylori. Full crystallographic information is available from OCA.
ReferenceReference
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
Page seeded by OCA on Thu Mar 20 13:43:40 2008