Structure of D-ribulose-l,5-bisphosphate carboxylase/oxygenase from Alcaligenes eutrophyus H16

RuBPcase, D-ribulose-1,5-bisphosphate carboxylase/oxygenase (EC4.1.1.39) is the key enzyme of the reductive pentose phosphate cycle. Because of its biological significance, many structural studies on a number of plant and bacterial RuBPCases have been undertaken, including the enzyme isolated from the autotrophic hydrogen-oxidizing bacterium Alcaligenes eutrophus H16 (refs 2-6). Although both the higher plant enzyme and the A. eutrophus enzyme consist of eight large and eight small subunits (L(8)S(8)), no model describing the quaternary structure is generally accepted. Here we present a model for the A. eutrophus RuBPCase derived from X-ray crystallography of three-dimensional (3D) crystals, and electron microscopy and image analysis of two-dimensional (2D) crystals of the enzyme. The X-ray electron density of RuBPCase in the presence of HCO(-)(3), Mg(2+), and the transition state analogue 2-carboxyarabinitol-1,5-bisphosphate (CABP) shows an L(8)S(8) molecule in which the L(4)S(4) half molecules have local 4-fold symmetry (C4). The local 4-fold axes of the two L(4)S(4) halves do not coincide but are shifted by 36 Å and are related by a crystallographic 2-fold axis perpendicular to and between the local 4-fold axes. Electron microscope data of the enzyme without CABP, which can be perfectly modelled using the X-ray densities, do not show this shift and the low-resolution point group of the molecules in the 2D crystals is D4. Both structures are presented.