21IG

Crystal structure of terpeniod cyclase SpSODS from rhizobacterium Serratia plymuthica

21IG の概要

• エントリーDOI: 10.2210/pdb21ig/pdb
• 分子名称: Terpene synthase, GLYCEROL (3 entities in total)
• 機能のキーワード: terpeniod cyclase, sodorifen synthase, spsods, lyase
• 由来する生物種: Serratia plymuthica 4Rx13
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 84703.52

構造登録者

Li, X.Q.,Zheng, Y.,Zhang, L.L.,Huang, J.-W.,Chen, C.-C.,Guo, R.-T. (登録日: 2025-12-13, 公開日: 2026-03-18, 最終更新日: 2026-03-25)

主引用文献

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

実験手法

X-RAY DIFFRACTION (2.22 Å)