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

By Peter C. Loewen, Xavi Carpena, Carme Rovira, Anabella Ivancich, Rosa Perez-luque, Rainer Haas, Stefan Odenbreit, Peter Nicholls and Ignacio Fita

Abstract

ABSTRACT: 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 Å with crystallographic agreement factors R and Rfree of 17.4 and 21.9%, respectively. The crystal exhibits P21212 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 Å (with R and Rfree 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 th

Year: 2003
OAI identifier: oai:CiteSeerX.psu:10.1.1.320.5804
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