Heavy riboflavin synthase from Bacillus subtilis: Particle dimensions, crystal packing and molecular symmetry

Abstract

Heavy riboflavin synthase from Bacillus subtilis is an enzyme complex consisting of approximately three α-subunits ( M r 23.5 × 10 3) and 60 β-subunits ( M r 16 × 10 3). The enzyme has been crystallized from phosphate buffer in a hexagonal crystal modification that belongs to space group P6 322. The asymmetric unit of the crystal cell contains ten β-subunits. The structure of this unusual 10 6 M r protein has been studied by small-angle X-ray scattering, electron microscopy of three-dimensional crystals, and crystallographic methods. The scattering curves can be interpreted in terms of a hollow sphere model with a ratio of inner and outer radius of 0.3:1. A diameter of 168 Å was estimated from the scattering curves, in close agreement with electron microscopic studies. An aggregate with the stoichiometry β 60, which was obtained by ligand-driven reaggregation of isolated β-subunits, showed similar shape and dimensions, but a larger value for the ratio R i R a . Electron micrographs of freeze-etched enzyme crystals showed approximately spherical molecules, which were arranged in hexagonal layers. The lattice constants found from the micrographs are in good agreement with the values derived from X-ray diffraction data. Rotation function calculations in Patterson space showed a set of peaks for 2-fold, 3-fold and 5-fold local rotation axes, accurately consistent with icosahedral symmetry and with the particle orientation A shown in the Appendix. The crystal packing can be described as follows: enzyme particles with icosahedral symmetry (point group 532) are located at points 32 of the hexagonal cell, corresponding to positions (0,0,0) and (0,0, 1 2 ) on the 6-fold screw axes. From the data reported, it may be concluded that the enzyme structure can be described as an icosahedral capsid of 60 β-subunits with the triangulation number T = 1. The α-subunits are located in the central core space of the capsid, but their spatial orientation is incompletely understood.