7VTB

Partially closed conformation of talaropentaene synthase cyclase domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Discovery of non-squalene triterpenes.

Tao, H.Lauterbach, L.Bian, G.Chen, R.Hou, A.Mori, T.Cheng, S.Hu, B.Lu, L.Mu, X.Li, M.Adachi, N.Kawasaki, M.Moriya, T.Senda, T.Wang, X.Deng, Z.Abe, I.Dickschat, J.S.Liu, T.

(2022) Nature 606: 414-419

  • DOI: https://doi.org/10.1038/s41586-022-04773-3
  • Primary Citation of Related Structures:  
    7VTA, 7VTB, 7WIJ

  • PubMed Abstract: 

    All known triterpenes are generated by triterpene synthases (TrTSs) from squalene or oxidosqualene 1 . This approach is fundamentally different from the biosynthesis of short-chain (C 10 -C 25 ) terpenes that are formed from polyisoprenyl diphosphates 2-4 . In this study, two fungal chimeric class I TrTSs, Talaromyces verruculosus talaropentaene synthase (TvTS) and Macrophomina phaseolina macrophomene synthase (MpMS), were characterized. Both enzymes use dimethylallyl diphosphate and isopentenyl diphosphate or hexaprenyl diphosphate as substrates, representing the first examples, to our knowledge, of non-squalene-dependent triterpene biosynthesis. The cyclization mechanisms of TvTS and MpMS and the absolute configurations of their products were investigated in isotopic labelling experiments. Structural analyses of the terpene cyclase domain of TvTS and full-length MpMS provide detailed insights into their catalytic mechanisms. An AlphaFold2-based screening platform was developed to mine a third TrTS, Colletotrichum gloeosporioides colleterpenol synthase (CgCS). Our findings identify a new enzymatic mechanism for the biosynthesis of triterpenes and enhance understanding of terpene biosynthesis in nature.


  • Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TvTS cyclase domain328Talaromyces verruculosusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NI
Query on NI

Download Ideal Coordinates CCD File 
B [auth A]NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.183 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.809α = 90
b = 61.942β = 116.298
c = 81.297γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-06-08
    Type: Initial release
  • Version 1.1: 2022-06-15
    Changes: Database references
  • Version 1.2: 2022-06-22
    Changes: Database references
  • Version 1.3: 2023-11-29
    Changes: Data collection, Refinement description