Structure and catalytic mechanism of C₁₆ terpenoid cyclase SpSODS from Serratia plymuthica

Terpenoid cyclases (TCs) utilize acyclic linear C_5n precursors as substrates to synthesize structurally diverse terpenoids that contain mono- or polycyclic carbon skeletons. A C₁₆ terpenoid cyclase SpSODS from Rhizobacterium Serratia plymuthica 4R×13 transforms the monocyclic α-pre-sodorifen pyrophosphate (α-PSPP, C₁₆) to homoterpenoid sodorifen with a bicyclo[3.2.1]octadiene skeleton. Here, we report the crystal structure of SpSODS and its complexes with pyrophosphate (PPi) and substrate analogue geranyl pyrophosphate (GPP) in a closed conformation. These structures reveal the conformational transitions between the open and closed states, and demonstrate the residues involved in the substrate-interaction network. Combining the mutagenesis experiments and the docking assays, we inferred key residues that could play an essential role in each step of the previously proposed sodorifen synthesis process. Notably, a water molecule that is stabilized by Y318, N241, and R237, and invariantly seen in all resolved structures might involve in the deprotonation at the final stage of the reaction. These findings provide insight into the structure and catalytic mechanism of SpSODS and lay an important foundation for future investigations of this type of non-canonical TCs.