21IG

Crystal structure of terpeniod cyclase SpSODS from rhizobacterium Serratia plymuthica

Summary for 21IG

• Entry DOI: 10.2210/pdb21ig/pdb
• Descriptor: Terpene synthase, GLYCEROL (3 entities in total)
• Functional Keywords: terpeniod cyclase, sodorifen synthase, spsods, lyase
• Biological source: Serratia plymuthica 4Rx13
• Total number of polymer chains: 2
• Total formula weight: 84703.52

Authors

Li, X.Q.,Zheng, Y.,Zhang, L.L.,Huang, J.-W.,Chen, C.-C.,Guo, R.-T. (deposition date: 2025-12-13, release date: 2026-03-18, Last modification date: 2026-03-25)

Primary citation

Li, X.,Zhang, L.,Zheng, Y.,Pan, N.,Zhou, Z.,Huang, Y.,Liang, Q.,Huang, J.W.,Chen, C.C.,Guo, R.T.
Structure and catalytic mechanism of C 16 terpenoid cyclase SpSODS from Serratia plymuthica.
Int.J.Biol.Macromol., 352:151065-151065, 2026

PubMed Abstract: Terpenoid cyclases (TCs) utilize acyclic linear C precursors as substrates to synthesize structurally diverse terpenoids that contain mono- or polycyclic carbon skeletons. A C terpenoid cyclase SpSODS from Rhizobacterium Serratia plymuthica 4R×13 transforms the monocyclic α-pre-sodorifen pyrophosphate (α-PSPP, C) 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.

PubMed: 41747984
DOI: 10.1016/j.ijbiomac.2026.151065

Experimental method

X-RAY DIFFRACTION (2.22 Å)