7XKW

The 3D strcuture of (-)-cyperene synthase with substrate analogue FSPP

Summary for 7XKW

• Entry DOI: 10.2210/pdb7xkw/pdb
• EMDB information: 33209
• Descriptor: (-)-cyperene synthase, S-[(2E,6E)-3,7,11-TRIMETHYLDODECA-2,6,10-TRIENYL] TRIHYDROGEN THIODIPHOSPHATE, MAGNESIUM ION (3 entities in total)
• Functional Keywords: (-)-cyperene synthase, cyclization mechanism, directed evolution, alphafold2, plant protein
• Biological source: Artabotrys hexapetalus
• Total number of polymer chains: 1
• Total formula weight: 65712.76

Authors

Yu, S.S.,Zhu, P.,Liu, Y.B.,Ma, S.G.,Ye, D.,Shao, Y.Z.,Li, W.R.,Cui, Z.J. (deposition date: 2022-04-20, release date: 2023-10-25, Last modification date: 2025-07-02)

Primary citation

Ye, D.,Shao, Y.Z.,Li, W.R.,Cui, Z.J.,Gong, T.,Yang, J.L.,Wang, H.Q.,Dai, J.G.,Feng, K.P.,Ma, M.,Ma, S.G.,Liu, Y.B.,Zhu, P.,Yu, S.S.
Characterization and Engineering of Two Highly Paralogous Sesquiterpene Synthases Reveal a Regioselective Reprotonation Switch.
Angew.Chem.Int.Ed.Engl., 63:e202315674-e202315674, 2024

PubMed Abstract: Sesquiterpene synthases (STPSs) catalyze carbocation-driven cyclization reactions that can generate structurally diverse hydrocarbons. The deprotonation-reprotonation process is widely used in STPSs to promote structural diversity, largely attributable to the distinct regio/stereoselective reprotonations. However, the molecular basis for reprotonation regioselectivity remains largely understudied. Herein, we analyzed two highly paralogous STPSs, Artabotrys hexapetalus (-)-cyperene synthase (AhCS) and ishwarane synthase (AhIS), which catalyze reactions that are distinct from the regioselective protonation of germacrene A (GA), resulting in distinct skeletons of 5/5/6 tricyclic (-)-cyperene and 6/6/5/3 tetracyclic ishwarane, respectively. Isotopic labeling experiments demonstrated that these protonations occur at C3 and C6 of GA in AhCS and AhIS, respectively. The cryo-electron microscopy-derived AhCS complex structure provided the structural basis for identifying different key active site residues that may govern their functional disparity. The structure-guided mutagenesis of these residues resulted in successful functional interconversion between AhCS and AhIS, thus targeting the three active site residues [L311-S419-C458]/[M311-V419-A458] that may act as a C3/C6 reprotonation switch for GA. These findings facilitate the rational design or directed evolution of STPSs with structurally diverse skeletons.

PubMed: 38327006
DOI: 10.1002/anie.202315674

Experimental method

ELECTRON MICROSCOPY (3.1 Å)