Crystal structure of a novel-type archaeal Rubisco with pentagonal symmetry

Background: Ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the key enzyme of the Calvin-Benson cycle and catalyzes the primary reaction of CO2 fixation in plants, algae, and bacteria. Rubiscos have been so far classified into two types. Type I is composed of eight large subunits (L subunits) and eight small subunits (S subunits) with tetragonal symmetry (L8S8), but type II is usually composed only of two L subunits (L-2). Recently, some genuinely active Rubiscos of unknown physiological function have been reported from archaea. Results: The crystal structure of Rubisco from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 (Tk-Rubisco) was determined at 2.8 a resolution. The enzyme is composed only of L subunits and showed a novel (L-2)(5) decameric structure. Compared to previously known type I enzymes, each L-2 dimer is inclined approximately 16 degrees to form a toroid-shaped decamer with its unique L-2-L-2 interfaces. Differential scanning calorimetry (DSC), circular dichroism (CD), and gel permeation chromatography (GPC) showed that Tk-Rubisco maintains its secondary structure and decameric assembly even at high temperatures. Conclusions: The present study provides the first structure of an archaeal Rubisco, an unprecedented (L-2)(5) decamer. Biochemical studies indicate that Tk-Rubisco maintains its decameric structure at high temperatures. The structure is distinct from type I and type II Rubiscos and strongly supports that Tk-Rubisco should be classified as a novel type III Rubisco.