7XKW | pdb_00007xkw

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Characterization and Engineering of Two Highly Paralogous Sesquiterpene Synthases Reveal a Regioselective Reprotonation Switch.

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.

(2024) Angew Chem Int Ed Engl 63: e202315674-e202315674

  • DOI: https://doi.org/10.1002/anie.202315674
  • Primary Citation Related Structures: 
    7XKW

  • 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.


  • Organizational Affiliation
    • State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100050, People's Republic of China.

Macromolecule Content 

  • Total Structure Weight: 65.71 kDa 
  • Atom Count: 4,132 
  • Modeled Residue Count: 499 
  • Deposited Residue Count: 561 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
(-)-cyperene synthase561Artabotrys hexapetalusMutation(s): 0 
UniProt
Find proteins for A0AAJ6N5X9 (Artabotrys hexapetalus)
Explore A0AAJ6N5X9 
Go to UniProtKB:  A0AAJ6N5X9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AAJ6N5X9
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China21732008
Other governmentChinaCIFMS-2021-I2M-1-029
Other governmentChina2018YFA0901900

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-25
    Type: Initial release
  • Version 1.1: 2024-03-27
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Database references
  • Version 1.3: 2025-07-02
    Changes: Data collection, Structure summary