Crystallization and X-ray diffraction analysis of a putative bacterial class I labdane-related diterpene synthase

Labdane-related diterpenoids are natural products with potential pharmaceutical applications that are rarely found in bacteria. Here, a putative class I labdane-related diterpene synthase (LrdC) identified by genome mining in a streptomycete was successfully crystallized using the microbatch method. Crystals of the LrdC enzyme were obtained in a holo form with its natural cofactor Mg²⁺ (LrdC-Mg²⁺) and in complex with inorganic pyrophosphate (PP_i) (LrdC-Mg²⁺–PP_i). Crystals of native LrdC-Mg²⁺ diffracted to 2.50 Å resolution and belonged to the trigonal space group P3₂21, with unit-cell parameters a = b = 107.1, c = 89.2 Å. Crystals of the LrdC-Mg²⁺–PP_i complex grown in the same conditions as the native enzyme with PEG 8000 diffracted to 2.36 Å resolution and also belonged to the trigonal space group P3₂21. Crystals of the LrdC-Mg²⁺–PP_i complex grown in a second crystallization condition with PEG 3350 diffracted to 2.57 Å resolution and belonged to the monoclinic space group P2₁, with unit-cell parameters a = 49.9, b = 104.1, c = 66.5 Å, β = 111.4°. The structure was determined by the single-wavelength anomalous dispersion (SAD) technique using the osmium signal from a potassium hexachloroosmate (IV) derivative.