CRYSTALLOGRAPHIC STRUCTURE OF A PLP-DEPENDENT ORNITHINE DECARBOXYLASEFROM LACTOBACILLUS-30A TO 3.0 ANGSTROM RESOLUTION

Ornithine decarboxylase from Lactobacillus 30a (L30a OrnDC) is represe ntative of the large, pyridoxal-5'-phosphate-dependent decarboxylases that act on lysine, arginine or ornithine. The crystal structure of th e L30a OrnDC has been solved to 3.0 Angstrom resolution using MIR phas es in combination with density modification (space group P6; a = 195.6 Angstrom, c = 97.6 Angstrom; dimer of 1460 amino acid residues/asymme tric unit; V-M = 3.26 Angstrom(3)/Da). The refined crystallographic R- value was 0.219 (R(free) = 0.268) using 2-fold restraints with a 4 sig ma cutoff and 8.0 to 3.0 Angstrom resolution data. Six dimers related by C6 symmetry compose the enzymatically active dodecamer (similar to 10(6) Da). Each monomer of L30a OrnDC can be described in terms of fiv e sequential folding domains. The amino-terminal domain, residues 1 to 107, consists of a five-stranded beta-sheet termed the ''wing'' domai n. Two wing domains of each dimer project inward towards the center of the dodecamer and contribute to dodecamer stabilization. The ''linker '' domain, residues 108 to 160, consists of short alpha-helices separa ted by a loop that fills in the PLP pocket. The third domain, residues 161 to 413, is an alpha/beta domain containing a seven stranded beta- sheet that resembles the PLP-binding domain of the aspartate aminotran sferases. The fourth domain, residues 414 to 569, resembles the ''smal l'' domain of the aspartate aminotransferases, but is significantly la rger due to insertions. The remaining carboxy-terminal domain, residue s 570 to 730, is organized into multiple antiparallel loops and seven alpha-helices that help form a deep channel leading to the PLP-binding site. (C) 1995 Academic Press Limited