Structural studies of acetoacetate decarboxylase

The bacterium Clostridium acetobutylicum relies on the enzyme acetoacetate decarboxylase (AADase) for pH homeostasis in the cell. AADase produces acetone and CO2 from acetoacetate. Historically, the by-product, acetone, was important in a variety of industrial processes, including arms production. In what is perhaps the first purposeful biotechnology application, the British devised a method to use AADase for the production of acetone during World War I. In 1968, Dr. F.H. Westheimer and his colleagues determined that the pKa of the active-site lysine is 4.5 units below that of lysine in solution. It was hypothesized that the perturbation of the lysine pKa was caused by the proximity to an adjacent lysine. This electrostatic perturbation hypothesis has been confirmed in other enzymes, but never for AADase the enzyme that gave rise to the theory.; The X-ray structure of Chromobacterium violaceum AADase (AAD_chv), a homologue of the C. acetobutylicum enzyme (AAD_cla), was solved via phasing by multiple wavelength anomalous diffraction using selenomethionine-labelled protein to 2.1A resolution. The structure of AAD_chv was then used as the search model to solve the structure of AAD_cla by molecular replacement to 2.4A resolution. The crystal structures show that AAD_cla possesses a novel protein fold and revealed that the hydrophobic core is responsible for the perturbation of the active-site lysine pK a and not the adjacent lysine. Additionally, the X-ray structures of unliganded AAD_chv plus liganded AAD_chv at 2.1A resolution suggest a detailed mechanism for beta-decarboxylation by AADase, in which Arg30 (AAD_cla numbering) acts to make a weak salt bridge with the substrate, positioning it for Schiff-base formation. The existence of two alternate rotamer positions for Glu76 suggests the carboxylate side chain may destabilize the carboxylate of the substrate and thus facilitate decarboxylation to form the neutral products, acetone and CO2.; The dodecameric enzyme complex possesses tetrahedral symmetry, an extremely rare arrangement. Prior to solving the crystal structure of AAD_cla using molecular replacement, a combination of EM and X-ray diffraction data and NCS phase extension were attempted but failed to provide adequate phasing. Using the crystal structure of AAD_cla, we were able to retrospectively analyze why these methods failed.