Structure of Helicobacter pylori Catalase, with and without Formic Acid Bound, at 1.6 Å Resolution

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• 作者：Peter C. Loewen ; Xavi Carpena ; Carme Rovira ; Anabella Ivancich ; Rosa Perez-Luque ; Rainer Haas ; Stefan Odenbreit ; Peter Nicholls ; and Ignacio Fita
• 刊名：Biochemistry
• 出版年：2004
• 出版时间：March 23, 2004
• 年：2004
• 卷：43
• 期：11
• 页码：3089 - 3103
• 全文大小：1114K
• 年卷期：v.43,no.11(March 23, 2004)
• ISSN：1520-4995

文摘

Helicobacter pylori produces one monofunctional catalase, encoded by katA (hp0875). Thecrystal structure of H. pylori catalase (HPC) has been determined and refined at 1.6 Å with crystallographicagreement factors R and R_free of 17.4 and 21.9%, respectively. The crystal exhibits P2₁2₁2 space groupsymmetry 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 aperhydroxy or dioxygen group in a compound III-like structure. Formic acid is known to bind in theactive site of catalases, promoting the breakdown of reaction intermediates compound I and compoundII. The structure of an HPC crystal soaked with sodium formate at pH 5.6 has also been determined to 1.6Å (with R and R_free values of 18.1 and 20.7%, respectively), revealing at least 36 separate formate orformic acid residues in the HPC dimer. In turn, the number of water molecules refined into the modelsdecreased from 1016 in the native enzyme to 938 in the formate-treated enzyme. Extra density, interpretedas azide, is found in a location of both structures that involves interaction with all four subunits in thetetramer. Electron paramagnetic resonance spectra confirm that azide does not bind as a ligand of the ironand that formate does bind in the heme pocket. The stability of the formate or formic acid moleculefound inside the heme distal pocket has been investigated by calculations based on density functionaltheory.