8YL9

Crystal structures of terpene synthases complexed with a substrate mimic


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.193 

Starting Model: in silico
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Literature

Structural Insights Into the Terpene Cyclization Domains of Two Fungal Sesterterpene Synthases and Enzymatic Engineering for Sesterterpene Diversification.

Xu, M.Xu, H.Lei, Z.Xing, B.Dickschat, J.S.Yang, D.Ma, M.

(2024) Angew Chem Int Ed Engl 63: e202405140-e202405140

  • DOI: https://doi.org/10.1002/anie.202405140
  • Primary Citation of Related Structures:  
    8YL9, 8YLA

  • PubMed Abstract: 

    Little is known about the structures and catalytic mechanisms of sesterterpene synthases (StTSs), which greatly hinders the structure-based engineering of StTSs for structural diversity expansion of sesterterpenes. We here report on the crystal structures of the terpene cyclization (TC) domains of two fungal StTSs: sesterfisherol synthase (NfSS) and sesterbrasiliatriene synthase (PbSS). Both TC structures contain benzyltriethylammonium chloride (BTAC), pyrophosphate (PPi), and magnesium ions (Mg 2+ ), clearly defining the catalytic active sites. A combination of theory and experiments including carbocationic intermediates modeling, site-directed mutagenesis, and isotope labeling provided detailed insights into the structural basis for their catalytic mechanisms. Structure-based engineering of NfSS and PbSS resulted in the formation of 20 sesterterpenes including 13 new compounds and four pairs of epimers with different configurations at C18. These results expand the structural diversity of sesterterpenes and provide important insights for future synthetic biology research.


  • Organizational Affiliation

    State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Haidian District, Beijing, 100191, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sesterbrasiliatriene synthase PbSSA,
B,
C [auth I]
352Penicillium brasilianumMutation(s): 0 
Gene Names: PbSS
EC: 4.2.3 (PDB Primary Data), 2.5.1.29 (PDB Primary Data), 2.5.1.81 (PDB Primary Data)
UniProt
Find proteins for A0A2Z6AQX7 (Penicillium brasilianum)
Explore A0A2Z6AQX7 
Go to UniProtKB:  A0A2Z6AQX7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2Z6AQX7
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 
H [auth A],
M [auth B],
R [auth I]
N-benzyl-N,N-diethylethanaminium
C13 H22 N
VBQDSLGFSUGBBE-UHFFFAOYSA-N
PPV (Subject of Investigation/LOI)
Query on PPV

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
Q [auth I]
PYROPHOSPHATE
H4 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.193 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.99α = 90
b = 146.99β = 90
c = 146.99γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2024-04-24 
  • Deposition Author(s): Xu, M., Ma, M.

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

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-24
    Type: Initial release
  • Version 1.1: 2024-06-05
    Changes: Database references
  • Version 1.2: 2024-06-12
    Changes: Database references