2IQF

Crystal structure of Helicobacter pylori catalase compound I

Summary for 2IQF

• Entry DOI: 10.2210/pdb2iqf/pdb
• Related: 1QWL 1QWM
• Descriptor: Catalase, ACETATE ION, PROTOPORPHYRIN IX CONTAINING FE, ... (5 entities in total)
• Functional Keywords: hydroxoferryl heme, beta barrel, oxidoreductase
• Biological source: Helicobacter pylori
• Cellular location: Cytoplasm (Probable): P77872
• Total number of polymer chains: 2
• Total formula weight: 118912.10

Authors

Loewen, P.C.,Carpena, X.,Fita, I. (deposition date: 2006-10-13, release date: 2007-08-28, 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., 129:4193-4205, 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 (1.86 Å)