8DAE | pdb_00008dae

Arabidopsis thaliana bifunctional dihydrofolate reductase-thymidylate synthase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.237 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.202 (Depositor), 0.210 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into a plant-conserved DHFR-TS reveal a selective herbicide target.

Haywood, J.Breese, K.J.McDougal, D.P.Verdonk, C.Partridge, A.Lo, A.F.Zhang, J.Yang, W.C.Bruning, J.B.Saliba, K.J.Bond, C.S.Stubbs, K.A.Mylne, J.S.

(2025) Mol Plant 18: 1294-1309

  • DOI: https://doi.org/10.1016/j.molp.2025.06.016
  • Primary Citation of Related Structures:  
    8DAE

  • PubMed Abstract: 

    Modern agricultural practices rely on herbicides to reduce yield losses. Herbicide-resistant weeds threaten herbicide utility and, hence, food security. New herbicide modes of action and integrated pest-management practices are vital to mitigate this threat. As the antimalarials that target the bifunctional enzyme dihydrofolate reductase-thymidylate synthase (DHFR-TS) have been shown to be herbicidal, DHFR-TS might represent a mode-of-action target for the development of herbicides. Here, we present the crystal structure of a DHFR-TS (AtDHFR-TS1) from the model dicot Arabidopsis thaliana. It shows a divergent DHFR active site and a linker domain that challenges previous classifications of bifunctional DHFR-TS proteins. This plant-conserved architecture enabled us to develop highly selective herbicidal inhibitors of AtDHFR-TS1 over human DHFR and identify inhibitors with unique scaffolds via a large-library virtual screen. These results suggest that DHFR-TS is a viable herbicide target.


  • Organizational Affiliation
    • School of Molecular Sciences, The University of Western Australia, 35 Stirling Highway, Crawley, Perth, WA 6009, Australia; Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Kent Street, Bentley, Perth, WA 6102, Australia. Electronic address: joel.haywood@curtin.edu.au.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bifunctional dihydrofolate reductase-thymidylate synthase 1536Arabidopsis thalianaMutation(s): 0 
Gene Names: THY-1At2g16370F16F14.13
EC: 1.5.1.3 (PDB Primary Data), 2.1.1.45 (PDB Primary Data)
UniProt
Find proteins for Q05762 (Arabidopsis thaliana)
Explore Q05762 
Go to UniProtKB:  Q05762
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ05762
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.237 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.202 (Depositor), 0.210 (DCC) 
Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.717α = 90
b = 80.717β = 90
c = 181.757γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDE180101445
Australian Research Council (ARC)AustraliaDP190101048

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-21
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2026-02-04
    Changes: Database references, Structure summary