8ZWZ

terpene synthases with from Paramuricea clavata


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.296 (Depositor), 0.297 (DCC) 
  • R-Value Work: 
    0.260 (Depositor), 0.261 (DCC) 
  • R-Value Observed: 
    0.261 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Mining coral-derived terpene synthases and mechanistic studies of the coral biflorane synthase.

Chen, B.Mao, J.Xu, K.Liu, L.Lin, W.Guo, Y.W.Wu, R.Wang, C.Xu, B.

(2025) Sci Adv 11: eadv0805-eadv0805

  • DOI: https://doi.org/10.1126/sciadv.adv0805
  • Primary Citation of Related Structures:  
    8ZWZ

  • PubMed Abstract: 

    Biflorane diterpenoids are unique natural products often seen in marine animals. Recent studies have reported a small number of biflorane synthases. However, the catalytic mechanism and structural basis for biflorane formation remain unclear. To address these issues, we conducted genome mining of terpene synthases from the sea whip coral Paramuricea clavata , resulting in the discovery of a biflorane synthase Pc TS1. We performed a series of isotope labeling, crystallography, quantum mechanics/molecular mechanics calculations, and mutagenesis studies toward Pc TS1 to investigate the mechanism. Isotopic labeling studies, together with calculations, elucidate a cascade of 1,10-cyclization, 1,3-hydride shift, 1,6-cyclization, 1,2-hydride shift, 2,6-cyclization, cyclopropane ring opening, and deprotonation by the generated pyrophosphate, forming the biflorane scaffold. Crystallography, quantum mechanics/molecular mechanics, and mutagenesis studies confirmed the cascade and produced different terpene scaffolds. Our work demonstrated the mechanism of marine biflorane formation, elucidated the second crystal structure of a coral terpene synthase, and realized the terpene skeleton expansion.


  • Organizational Affiliation

    Shandong Laboratory of Yantai Drug Discovery, Bohai Rim Advanced Research Institute for Drug Discovery, Yantai, Shandong 264117, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Diterpene synthase412Paramuricea clavataMutation(s): 0 
Gene Names: PACLA_8A045082
UniProt
Find proteins for A0A6S7HXL7 (Paramuricea clavata)
Explore A0A6S7HXL7 
Go to UniProtKB:  A0A6S7HXL7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A6S7HXL7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.296 (Depositor), 0.297 (DCC) 
  • R-Value Work:  0.260 (Depositor), 0.261 (DCC) 
  • R-Value Observed: 0.261 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.284α = 90
b = 85.284β = 90
c = 106.137γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32270039

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release