The active center of catalase.
The refined structure of beef liver catalase (I. Fita, A. M. Silva, M. R. N. Murthy & M. G. Rossmann, unpublished results) is here examined with regard to possible catalytic mechanisms. The distal side of the deeply buried heme pocket is connected with the surface of the molecule by one (or possibly two) channel. The electron density representing the heme group, in each of the two crystallographically independent subunits, is consistent with degradation of the porphyrin rings. The heme group appears to be buckled, reflecting the high content of bile pigment in liver catalase. The spatial organization on the proximal side (where the fifth ligand of the iron is located) shows an elaborate network of interactions. The distal side contains the substrate pocket. The limited space in this region severely constrains possible substrate positions and orientations. The N delta atom of the essential His74 residue hydrogen bonds with O gamma of Ser113, which in turn hydrogen bonds to a water molecule associated with the propionic carbonylic group of pyrrole III. These interactions are also visible in the refined structure of Penicillium vitale catalase (B. K. Vainshtein, W. R. Melik-Adamyan, V. V. Barynin, A. A. Vagin, A. I. Grebenko, V. V. Borisov, K. S. Bartels, I. Fita, & M. G. Rossmann, unpublished results). Model building suggests a pathway for a catalase mechanism (compound I formation, as well as catalatic and peroxidatic reactions). There are some similarities in compound I formation of catalase and cytochrome c peroxidase.
D000595:Amino Acid Sequence; D000818:Animals; D001665:Binding Sites; D002374:Catalase; D002417:Cattle; D003461:Crystallography; D006418:Heme; D006860:Hydrogen Bonding; D008099:Liver / Q000201:enzymology; D046911:Macromolecular Substances; D008958:Models, Molecular; D008968:Molecular Conformation; D013696:Temperature
D046911:Macromolecular Substances; D006418:Heme; D002374:Catalase