2IUF

The structures of Penicillium vitale catalase: resting state, oxidised state (compound I) and complex with aminotriazole

Summary for 2IUF

• Entry DOI: 10.2210/pdb2iuf/pdb
• Descriptor: CATALASE, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose, CIS-HEME D HYDROXYCHLORIN GAMMA-SPIROLACTONE, ... (10 entities in total)
• Functional Keywords: oxidoreductase
• Biological source: PENICILLIUM JANTHINELLUM
• Total number of polymer chains: 2
• Total formula weight: 155347.83

Authors

Murshudov, G.,Borovik, A.,Grebenko, A.,Barynin, V.,Vagin, A.,Melik-Adamyan, W. (deposition date: 2006-06-02, release date: 2006-07-10, Last modification date: 2024-11-13)

Primary citation

Alfonso-Prieto, M.,Borovik, A.,Carpena, X.,Murshudov, G.,Melik-Adamyan, W.,Fita, I.,Rovira, C.,Loewen, P.C.
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.
J.Am.Chem.Soc., 129:4193-, 2007

PubMed 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.

PubMed: 17358056
DOI: 10.1021/JA063660Y

Experimental method

X-RAY DIFFRACTION (1.71 Å)