Structure of the Clade 1 Catalase, CatF of Pseudomonas syringae, at 1.8 Å Resolution

ringae has been identified phylogenetically as a clade 1 catalase, closely related to plant catalases, a group from which no structure has been determined. The structure of CatF has been refined at 1.8 Å resolution by using X-ray synchrotron data collected from a crystal flash-cooled with liquid nitrogen. The crystal-lographic agreement factors R and Rfree are, respec-tively, 18.3 % and 24.0%. The asymmetric unit of the crystal contains a whole molecule that shows accu-rate 222-point group symmetry. The crystallized en-zyme is ahomotetramer of subunitswith 484 residues, some 26 residues shorter than predicted from the DNAsequence.Mass spectrometryanalysis confirmed the absence of 26 N-terminal residues, possibly re-moved by a periplasmic transport system. The core structure of the CatF subunit was closely related to seven other catalases with root-mean-square devia-tions (RMSDs) of 368 coreC atoms of 0.99–1.30 Å. The heme component of CatF is heme b in the same orientation that is found inEscherichia colihydroper-oxidase II, an orientation that is flipped 180 ° with respect the orientation of the heme in bovine liver catalase. NADPH is not found in the structure of CatF because key residues required for nucleotide binding are missing; 2129 water molecules were refined into the model. Water occupancy in the main or perpen-dicular channel of CatF varied among the four sub-units from two to five in the region between the heme and the conserved Asp150. A comparison of the water occupancy in this region with the same region in other catalases reveals significant differences among the catalases. Proteins 2003;50:423–436