9KQW | pdb_00009kqw

eudesmanediol synthase complexed with Mg2+,PPi and BTAC(PeTS3 complex)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 
    0.228 (Depositor), 0.229 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.192 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Dihydroxy Terpene Synthase: Spatiotemporally Precise Manipulation of Water-Mediated Dihydroxylation via Stepwise Quenching of Carbocations.

Huang, Z.Y.Xu, K.Li, W.L.Li, C.X.Pan, J.Wu, R.Xu, J.H.

(2025) J Am Chem Soc 147: 45822-45831

  • DOI: https://doi.org/10.1021/jacs.5c19381
  • Primary Citation of Related Structures:  
    8X9C, 9KQW

  • PubMed Abstract: 

    Biosynthesis of hydroxy terpenes, which possess better solubility and target-binding capability than terpene hydrocarbons, generally needs cascaded catalysis of terpene synthase (TS) and cytochrome P450 oxygenase. Interestingly, some TSs can directly generate hydroxy terpenes (mostly monohydroxy terpenes) independent of oxygenases. There are even rare TSs that can form dihydroxy terpenes directly. Nevertheless, the structure and catalytic mechanism of dihydroxy terpene synthases (DHTSs) remain elusive to date, hindering their practical applications. Through protein crystallography, multiscale simulations, and site-directed mutagenesis, we elucidate a stepwise carbocation quenching mechanism. In this process, two water molecules are strictly manipulated by a dynamic hydrogen-bond network to quench the carbocation intermediates. Most importantly, Tyr312 was identified as the indispensable and irreplaceable residue for initiating the reprotonation of the monohydroxy terpene. The spatiotemporally precise manipulation mechanism of DHTSs enriches the knowledge of TSs and lays a foundation for developing an oxygenase-independent biosynthesis system of multihydroxy terpenes.


  • Organizational Affiliation
    • State Key Laboratory of Bioreactor Engineering, Shanghai Collaborative Innovation Centre for Biomanufacturing School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Terpenoid synthase
A, B
330Penicillium expansumMutation(s): 0 
Gene Names: PEX2_005160
UniProt
Find proteins for A0A0A2JK86 (Penicillium expansum)
Explore A0A0A2JK86 
Go to UniProtKB:  A0A0A2JK86
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0A2JK86
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BTM (Subject of Investigation/LOI)
Query on BTM

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B]
N-benzyl-N,N-diethylethanaminium
C13 H22 N
VBQDSLGFSUGBBE-UHFFFAOYSA-N
POP (Subject of Investigation/LOI)
Query on POP

Download Ideal Coordinates CCD File 
C [auth A],
H [auth B]
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
J [auth B]
K [auth B]
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
L [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free:  0.228 (Depositor), 0.229 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.192 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.37α = 90
b = 119.46β = 90
c = 123.31γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChina2019YFA0905000

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-22
    Type: Initial release
  • Version 1.1: 2025-12-24
    Changes: Database references