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

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 angstrom resolution, respectively. Despite the similar oxidation conditions employed, the iron-oxygen coordination length is 1.72 angstrom for PVC, close to what is expected for a FeO double bond, and 1.80 and 1.85 angstrom 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(center dot+)-(FeO)-O-IV, Por(center dot+)-(FeO)-O-IV center dot center dot center dot HisH(+), Por(center dot+)-Fe-IV-OH+ and Por-Fe-IV-OH (a protein radical is assumed in the latter configuration). The electronic structure of the primary oxidized species, Por(center dot+)-(FeO)-O-IV, differs qualitatively between HPC and PVC with an A(2u)-like porphyrin radical delocalized on the porphyrin in HPC and a mixed A(1u)-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(center dot+)-(FeO)-O-IV species with partial protonation of the distal histidine and compound I of HPC contains a hydroxoferryl Por-Fe-IV-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.