9MLO | pdb_00009mlo

Drimenol Synthase - Farnesyl Thiol Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free: 
    0.265 (Depositor), 0.265 (DCC) 
  • R-Value Work: 
    0.217 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.219 (Depositor) 

Starting Model: in silico
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Literature

Crystal structure and catalytic mechanism of drimenol synthase, an unusual bifunctional terpene cyclase-phosphatase.

Osika, K.R.Gaynes, M.N.Christianson, D.W.

(2025) Proc Natl Acad Sci U S A 122: e2506584122-e2506584122

  • DOI: https://doi.org/10.1073/pnas.2506584122
  • Primary Citation of Related Structures:  
    9MHS, 9MLO

  • PubMed Abstract: 

    Drimenol synthase from Aquimarina spongiae (AsDMS) is a highly unusual chimera that integrates two distinct, sequential isoprenoid processing activities within a single polypeptide chain. AsDMS catalyzes the class II cyclization of farnesyl diphosphate (FPP) to form drimenyl diphosphate, which then undergoes enzyme-catalyzed hydrolysis to yield drimenol, a bioactive sesquiterpene alcohol with antifungal and anticancer properties. Here, we report the X-ray crystal structures of AsDMS and its complex with a sesquiterpene thiol. The AsDMS structure exhibits a didomain architecture consisting of a terpene cyclase β domain and a haloacid dehalogenase-like phosphatase domain, with two distinct active sites located on opposite sides of the protein. Mechanistic studies show that dephosphorylation of the drimenyl diphosphate intermediate proceeds through stepwise hydrolysis such that two equivalents of inorganic phosphate rather than inorganic pyrophosphate are coproducts of the reaction sequence. When the AsDMS reaction is performed in H 2 18 O, 18 O is not incorporated into drimenol, indicating that the hydroxyl oxygen of drimenol originates from the prenyl oxygen of FPP rather than a water molecule from bulk solution. These results correct a mechanistic proposal previously advanced by another group. Surprisingly, AsDMS exhibits substrate promiscuity, catalyzing the conversion of the slowly reactive substrate mimic farnesyl- S -thiolodiphosphate into cyclic and linear sesquiterpene products. Structural and mechanistic insights gained from AsDMS illustrate the functional diversity of terpene biosynthetic enzymes and provide a foundation for engineering "designer cyclase" assemblies capable of generating a wide variety of terpenoid products.


  • Organizational Affiliation

    Department of Chemistry, Roy and Diana Vagelos Laboratories, University of Pennsylvania, Philadelphia, PA 19104-6323.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Haloacid dehalogenase superfamily, subfamily IA, variant 3 with third motif having DD or EDA [auth B],
B [auth A]
526Aquimarina spongiaeMutation(s): 0 
Gene Names: SAMN04488508_102320
UniProt
Find proteins for A0A1M6CXF0 (Aquimarina spongiae)
Explore A0A1M6CXF0 
Go to UniProtKB:  A0A1M6CXF0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1M6CXF0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BMF (Subject of Investigation/LOI)
Query on A1BMF

Download Ideal Coordinates CCD File 
E [auth B],
I [auth A]
(2E,6E)-3,7,11-trimethyldodeca-2,6,10-triene-1-thiol
C15 H26 S
CJWPDADGDASKGI-YFVJMOTDSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
H [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
PO4 (Subject of Investigation/LOI)
Query on PO4

Download Ideal Coordinates CCD File 
F [auth B],
J [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth B],
D [auth B],
G [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.64 Å
  • R-Value Free:  0.265 (Depositor), 0.265 (DCC) 
  • R-Value Work:  0.217 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.219 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 154.741α = 90
b = 154.741β = 90
c = 132.979γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
autoPROCdata reduction
Zanudadata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM56838

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-16
    Type: Initial release