9RP0

Ensemble refined structure of CotB2 in complex with 2-fluoro-3,7,18-dolabellatriene

Summary for 9RP0

• Entry DOI: 10.2210/pdb9rp0/pdb
• Descriptor: Cyclooctat-9-en-7-ol synthase, MAGNESIUM ION, PYROPHOSPHATE, ... (10 entities in total)
• Functional Keywords: terpene synthase, cyclooctatin, diterpence synthase, hydrolase
• Biological source: Streptomyces melanosporofaciens
• Total number of polymer chains: 2
• Total formula weight: 75987.59

Authors

Helmer, C.P.O.,Loll, B. (deposition date: 2025-06-23, release date: 2025-09-17, Last modification date: 2025-11-26)

Primary citation

Gupta, P.K.,Helmer, C.P.O.,Ringel, M.,Loll, B.,Bruck, T.,Major, D.T.
The initial dynamics of product release in terpene synthases-The case of CotB2.
Protein Sci., 34:e70312-e70312, 2025

PubMed Abstract: Although the enzymatic mechanisms of terpene synthases have been extensively characterized through experimental and computational studies, the atomistic details underlying the product release process have remained elusive. In this study, we present the first atomistic simulations of the initial stages of product release in a terpene synthase, using the bacterial diterpene cyclase CotB2 as a model system. CotB2 catalyzes the complex cyclization of geranylgeranyl diphosphate (GGDP) to the tricyclic diterpene cyclooctat-9-en-7-ol in a single active site through an 11-step reaction cascade. Our MD simulations focus on three model systems representing CotB2 with bound GGDP and cyclooctat-9-en-7-ol, the latter in two states-with the diphosphate fully deprotonated (PO ) and protonated diphosphate (HPO ). Analysis of the MD trajectories clearly shows that product release is initiated by the dislocation of the diphosphate group, which in turn triggers active site opening via coordinated C-terminal motions. Notably, protonation of the diphosphate moiety appears to be the key event that weakens its interactions with the active site and enables product release. These findings provide crucial mechanistic insight into the final phase of terpene biosynthesis and open new avenues for rational enzyme engineering targeting product release.

PubMed: 40990851
DOI: 10.1002/pro.70312

Experimental method

X-RAY DIFFRACTION (1.8 Å)