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Structure of the Clade 1 catalase, CatF of Pseudomonas syringae , at 1.8 Å resolution
Author(s) -
Carpena Xavi,
Soriano Manuel,
Klotz Martin G.,
Duckworth Harry W.,
Donald Lynda J.,
MelikAdamyan William,
Fita Ignacio,
Loewen Peter C.
Publication year - 2003
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10284
Subject(s) - homotetramer , crystallography , heme , chemistry , molecular replacement , stereochemistry , catalase , protein structure , protein subunit , crystal structure , biology , enzyme , biochemistry , gene
Catalase CatF of Pseudomonas syringae 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 crystallographic agreement factors R and R free are, respectively, 18.3% and 24.0%. The asymmetric unit of the crystal contains a whole molecule that shows accurate 222‐point group symmetry. The crystallized enzyme is a homotetramer of subunits with 484 residues, some 26 residues shorter than predicted from the DNA sequence. Mass spectrometry analysis confirmed the absence of 26 N‐terminal residues, possibly removed by a periplasmic transport system. The core structure of the CatF subunit was closely related to seven other catalases with root‐mean‐square deviations (RMSDs) of 368 core Cα atoms of 0.99–1.30 Å. The heme component of CatF is heme b in the same orientation that is found in Escherichia coli hydroperoxidase 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 perpendicular channel of CatF varied among the four subunits 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. © 2003 Wiley‐Liss, Inc.