The Structures and Electronic Configuration of Compound I Intermediates of Helicobacter pylori and Penicillium vitale Catalases Determined by X-ray Crystallography and QM/MM Density Functional Theory Calculations

• Published in: Journal of the American Chemical Society 2007-04, Vol.129 (14), p.4193-4205
• Main Authors: Alfonso-Prieto, Mercedes, Borovik, Anton, Carpena, Xavier, Murshudov, Garib, Melik-Adamyan, William, Fita, Ignacio, Rovira, Carme, Loewen, Peter C
• Format: Article
• Language: English
• Subjects: Binding Sites; Catalase - chemistry; Catalase - metabolism; Computer Simulation; Crystallography, X-Ray; Electrons; Helicobacter pylori - enzymology; Heme - analogs & derivatives; Heme - chemistry; Oxidation-Reduction; Penicillium - enzymology; Peroxidase - chemistry; Peroxidase - metabolism; Porphyrins - chemistry; Porphyrins - metabolism; Protein Binding
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/ja063660y

The structures of Helicobacter pylori (HPC) and Penicillium vitale (PVC) catalases, each with two subunits in the crystal asymmetric unit, oxidized with peroxoacetic acid are reported at 1.8 and 1.7 Å resolution, respectively. Despite the similar oxidation conditions employed, the iron−oxygen coordination length is 1.72 Å for PVC, close to what is expected for a FeO double bond, and 1.80 and 1.85 Å for HPC, suggestive of a Fe−O single bond. The structure and electronic configuration of the oxoferryl heme and immediate protein environment is investigated further by QM/MM density functional theory calculations. Four different active site electronic configurations are considered, Por•+−FeIVO, Por•+−FeIVO···HisH+, Por•+−FeIV−OH+ and Por−FeIV−OH (a protein radical is assumed in the latter configuration). The electronic structure of the primary oxidized species, Por•+−FeIVO, differs qualitatively between HPC and PVC with an A2u-like porphyrin radical delocalized on the porphyrin in HPC and a mixed A1u-like “fluctuating” radical partially delocalized over the essential distal histidine, the porphyrin, and, to a lesser extent, the proximal tyrosine residue. This difference is rationalized in terms of HPC containing heme b and PVC containing heme d. It is concluded that compound I of PVC contains an oxoferryl Por•+−FeIVO species with partial protonation of the distal histidine and compound I of HPC contains a hydroxoferryl Por−FeIV−OH with the second oxidation equivalent delocalized as a protein radical. The findings support the idea that there is a relation between radical migration to the protein and protonation of the oxoferryl bond in catalase.