Structure of catalase HPII from Escherichia coli at 1.9 angstrom resolution

Catalase HPII from Escherichia,li, a homotetramer of subunits with 753 resi dues, coli, a homotetramer of subunits with 753 residues, is the largest kn own catalase, The structure of native HPII has been refined at 1.9 Angstrom resolution using X-ray synchrotron data collected from crystals hash-coole d with liquid nitrogen. The crystallographic agreement factors R and R-free are respectively 16.6% and 21.0%. The asymmetric unit of the crystal conta ins a whole molecule that shows accurate 222-point group symmetry. The stru cture of the central part of the HPII subunit gives a root mean square devi ation of 1.5 Angstrom for 477 equivalencies with beef liver catalase, Most of the additional 276 residues of HPII are located in either an extended N- terminal arm or in a C-terminal domain organized with a flavodoxin-like top ology A small number of mostly hydrophilic interactions stabilize the relat ive orientation between the C-terminal domain and the core of the enzyme. T he heme component of HPII is a cis-hydroxychlorin gamma-spirolactone in an orientation that is flipped 180 degrees with respect to the orientation of the heme found in beef liver catalase, The proximal ligand of the heme is T yr415 which is joined by a covalent bond between its CP atom and the N-delt a atom of His392, Over 2,700 well-defined solvent molecules have been ident ified filling a complex network of cavities and channels formed inside the molecule. Two channels lead close to the distal side heme pocket of each su bunit suggesting separate inlet and exhaust functions. The longest channel, that begins in an adjacent subunit, is over 50 Angstrom in length, and the second channel is about 30 Angstrom in length. A third channel reaching th e heme proximal side may provide access for the substrate needed to catalyz e the heme modification and His-Tyr bond formation, HPII does not bind NADP H and the equivalent region to the NADPH binding pocket of bovine catalase, partially occluded in HPII by residues 585-590, corresponds to the entranc e to the second channel. The heme distal pocket contains two solvent molecu les, and the one closer to the iron atom appears to exhibit high mobility o r low occupancy compatible with weak coordination. (C) 1999 Wiley-Liss, Inc .