Enzymatic and structural characterization of type II isopentenyl diphosphate isomerase from hyperthermophilic archaeon Thermococcus kodakaraensis

Enzymatic and thermodynamic characteristics of type II isopentenyl diphosphate (IPP):dimethylallyl diphosphate (DMAPP) isomerase (Tk-IDI) from Thermococcus kodakaraensis, which catalyzes the interconversion of IPP and DMAPP, were examined. FMN was tightly bound to Tk-IDI, and the enzyme required NADPH and Mg2+ for the isomerization in both directions. The melting temperature (Tm), the change of enthalpy (ΔHm), and the heat capacity change (ΔCp) of Tk-IDI were 88.0 °C, 444 kJ mol−1, and 13.2 kJ mol−1 K−1, respectively, indicating that Tk-IDI is fairly thermostable. Kinetic parameters dramatically changed when the temperature crossed 80 °C even though its native overall structure was stably maintained up to 90 °C, suggesting that local conformational change would occur around 80 °C. This speculation was supported by the result of the circular dichroism analysis that showed the shift of the α-helical content occurred at 80 °C.