title: 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.
abstract: 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 A resolution, respectively. Despite the similar oxidation conditions employed, the iron-oxygen coordination length is 1.72 A for PVC, close to what is expected for a Fe=O double bond, and 1.80 and 1.85 A 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.
authors.affiliation: Centre especial de Recerca en Química Teorica, Parc Científic de Barcelona, Josep Samitier 1-5, 08028 Barcelona, Spain.
authors.forename: Mercedes
authors.initials: M
authors.lastname: Alfonso-Prieto
authors.forename: Anton
authors.initials: A
authors.lastname: Borovik
authors.forename: Xavier
authors.initials: X
authors.lastname: Carpena
authors.forename: Garib
authors.initials: G
authors.lastname: Murshudov
authors.forename: William
authors.initials: W
authors.lastname: Melik-Adamyan
authors.forename: Ignacio
authors.initials: I
authors.lastname: Fita
authors.forename: Carme
authors.initials: C
authors.lastname: Rovira
authors.forename: Peter C
authors.initials: PC
authors.lastname: Loewen
mesh_terms: D001665:Binding Sites; D002374:Catalase / Q000737:chemistry* / Q000378:metabolism*; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D004583:Electrons; D016480:Helicobacter pylori / Q000201:enzymology*; D006418:Heme / Q000031:analogs & derivatives / Q000737:chemistry; D010084:Oxidation-Reduction; D010407:Penicillium / Q000201:enzymology*; D009195:Peroxidase / Q000737:chemistry / Q000378:metabolism; D011166:Porphyrins / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding
chemical_list: D011166:Porphyrins; D006418:Heme; C080647:heme d; D002374:Catalase; D009195:Peroxidase