9LPB | pdb_00009lpb

Terpene cyclase AriE mutant-D128A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free: 
    0.204 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.179 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Crystal Structure and Catalytic Mechanism of the cis-Eunicellane Cyclase AriE.

Li, F.R.Yang, Q.He, J.Sun, X.Pan, X.Xu, H.M.Rudolf, J.D.Dong, L.B.

(2025) Chemistry 31: e202500012-e202500012

  • DOI: https://doi.org/10.1002/chem.202500012
  • Primary Citation of Related Structures:  
    9LPB

  • PubMed Abstract: 

    Eunicellane diterpenoids, with over 360 known examples characterized by a cis- or trans-6/10-bicyclic carbon skeleton, exhibit diverse biological activities. To date, five eunicellane cyclases (ECs) have been reported: cis-ECs (Bnd4, CpDTS2 and EcTPS1) and trans-ECs (AlbS and MicA), yet the structural basis and molecular mechanisms governing their distinct cis- or trans-cyclization modes remain unsolved. Here, we present the crystal structure of a cis-EC AriE from Amycolatopsis arida, which catalyzes geranylgeranyl diphosphate to form cis-6/10-fused bicyclic benditerpe-2,6,15-triene (1) in aridacin biosynthesis. Through surface entropy reduction, we obtained the 1.87 Å resolution structure of AriED128A. Structure-guided mutagenesis identified W73 as a key regulatory hotspot controlling product diversity, with its variants generating diverse diterpene products. Y203A converted AriE into a highly specific (-)-(R)-cembrene A synthase. Our findings provide the first structural insights into this type of terpene synthase and demonstrate the feasibility of engineering EC variants for selective product formation.


  • Organizational Affiliation
    • China Pharmaceutical University, School of Traditional Chinese Pharmacy, CHINA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Terpene synthase369Amycolatopsis aridaMutation(s): 1 
Gene Names: SAMN05421810_102118
EC: 4.2.3
UniProt
Find proteins for A0A1I5P1T3 (Amycolatopsis arida)
Explore A0A1I5P1T3 
Go to UniProtKB:  A0A1I5P1T3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1I5P1T3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.87 Å
  • R-Value Free:  0.204 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.179 (Depositor), 0.179 (DCC) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.815α = 90
b = 83.815β = 90
c = 163.673γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
iMOSFLMdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82073746

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-07
    Type: Initial release
  • Version 1.1: 2025-06-11
    Changes: Database references