9E2H | pdb_00009e2h

Variediene synthase hexameric prenyltransferase core


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.77 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of bifunctional variediene synthase yields unique insight on biosynthetic diterpene assembly and cyclization.

Wenger, E.S.Christianson, D.W.

(2025) Nat Commun 16: 5089-5089

  • DOI: https://doi.org/10.1038/s41467-025-60537-3
  • Primary Citation of Related Structures:  
    9E2H, 9E2I, 9E2J, 9E2K, 9E2L, 9E2M

  • PubMed Abstract: 

    An unusual family of bifunctional terpene synthases has been identified in which a prenyltransferase assembles 5-carbon precursors to form C 20 geranylgeranyl diphosphate (GGPP), which is then converted into a polycyclic product by a cyclase. Here, we report the cryo-EM structure of a massive, 495-kD bifunctional terpene synthase, variediene synthase from Emericella variecolor (EvVS). The structure reveals a hexameric prenyltransferase core sandwiched between two triads of cyclases. Surprisingly, GGPP is not channeled intramolecularly from the prenyltransferase to the cyclase, but instead is channeled intermolecularly to a non-native cyclase as indicated by substrate competition experiments. These results inform our understanding of carbon management in the greater family of bifunctional terpene synthases, hundreds of which have been identified in fungi. Using sequence similarity networks, we also report the identification of bifunctional terpene synthases in an animal, Adineta steineri, a bdelloid rotifer indigenous to freshwater environments.


  • Organizational Affiliation
    • Department of Chemistry, Roy and Diana Vagelos Laboratories, University of Pennsylvania, Philadelphia, PA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Variediene synthase
A, B, C, D, E
A, B, C, D, E, F
725Aspergillus stellatusMutation(s): 0 
Gene Names: EvVS
EC: 4.2.3.218 (PDB Primary Data), 4.2.3.219 (PDB Primary Data), 2.5.1.29 (PDB Primary Data), 2.5.1.81 (PDB Primary Data)
UniProt
Find proteins for A0A0P0ZD79 (Emericella variicolor)
Explore A0A0P0ZD79 
Go to UniProtKB:  A0A0P0ZD79
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0P0ZD79
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.77 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States574961-0089

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release
  • Version 1.1: 2025-12-03
    Changes: Data collection, Database references