9KGB

Crystal structure of tolypothrichol synthase

Summary for 9KGB

• Entry DOI: 10.2210/pdb9kgb/pdb
• Descriptor: terpene synthase, SULFATE ION (3 entities in total)
• Functional Keywords: terpene synthase, diterpene cyclase, scytonema tolypothrichoides vb-61278, biosynthetic protein
• Biological source: Scytonema tolypothrichoides VB-61278
• Total number of polymer chains: 1
• Total formula weight: 42519.52

Authors

Yu, J.,Shiraishi, T.,Yoshida, A.,Kuzuyama, T. (deposition date: 2024-11-08, release date: 2025-04-09, Last modification date: 2025-04-16)

Primary citation

Yu, J.,Shiraishi, T.,Taizoumbe, K.A.,Karasuno, Y.,Yoshida, A.,Nishiyama, M.,Dickschat, J.S.,Kuzuyama, T.
Mechanistic Characterization of Diterpene Synthase Pairs for Tricyclic Diterpenes from Cyanobacteria.
J.Am.Chem.Soc., 147:11896-11905, 2025

PubMed Abstract: In recent years, genome mining in cyanobacteria has revealed abundant gene clusters related to natural product biosynthesis. However, only a few terpene synthases (TSs) have been identified from this bacterial phylum. Pfam profiles, such as PF03936 and PF19086, which are frequently used for TS retrieval, are built from plant, bacterial, and fungal TSs. Herein, we constructed a new hidden Markov model (HMM) specific to bacterial TSs on the basis of 110 bacterial TSs experimentally validated in recent years. Using this model, we identified a pair of diterpene synthases, Cpt11 (class II TS) and Cts11 (class I TS), in the cyanobacterium . experiments demonstrated that Cpt11 catalyzes the formation of -copalyl diphosphate from geranylgeranyl diphosphate and that Cts11 subsequently converts -copalyl diphosphate into a rare 6,6,7-tricyclic diterpene alcohol. Its biosynthesis was established through isotope labeling experiments, which revealed a unique sequence of a 1,6-proton shift and ring expansion to a seven-membered ring. We solved the crystal structure of Cts11 at a resolution of 1.76 Å. Additionally, via site-directed mutagenesis experiments, we identified two amino acid residues whose exchanges affected the formation of the original diterpene alcohol, leading to the formation of two new compounds: a 6,6,7-tricyclic diterpene hydrocarbon and another 6,6,6-tricyclic diterpene alcohol. A BLAST search revealed several sequences that shared over 70% identity with Cts11 from cyanobacteria that could produce diverse diterpenes. This study demonstrates the potential for cyanobacteria to produce unprecedented terpenoids and lays the foundation for studying the physiological activities of terpenoids in cyanobacteria.

PubMed: 40143759
DOI: 10.1021/jacs.4c16710

Experimental method

X-RAY DIFFRACTION (1.76 Å)