The atomic structure of pentameric lumazine synthase from Saccharomyces cerevisiae at 1.85 angstrom resolution reveals the binding mode of a phosphonate intermediate analogue

Lumazine synthase of Saccharomyces cerevisiae is a homopentamer with a mole cular weight of 90 kDa. Crystals of the recombinant enzyme with a size of u p to 1.6 mm were obtained. The space group is P4(1)2(1)2 with lattice dimen sions 82.9 Angstrom * 82.9 Angstrom * 300.2 Angstrom. X-ray diffraction dat a collected under cryogenic conditions were complete to 1.85 Angstrom resol ution. The structure of the enzyme in complex with the intermediate analogu e, 5-(6-D-ribitylamino-2,4-dihydroxypyrimidine-5-yl)-1-pentyl-phosphonic ac id was solved via molecular replacement using the structure of the Bacillus subtilis enzyme as search model and was refined to a final X-factor of 19. 8% (R-free:22.5%). The conformation of the active site ligand of the enzyme mimicks that of the Schiff base intermediate of the enzyme-catalyzed react ion. The data enable the reconstruction of the reactant topology during the early steps of the catalytic reaction. Structural determinants, which are likely to be responsible for the inability of the S. cerevisiae enzyme to f orm icosahedral capsids, will be discussed. (C) 2000 Academic Press.