7MDS

Crystal structure of AtDHDPS1 in complex with MBDTA-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.183 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Towards novel herbicide modes of action by inhibiting lysine biosynthesis in plants.

Soares da Costa, T.P.Hall, C.J.Panjikar, S.Wyllie, J.A.Christoff, R.M.Bayat, S.Hulett, M.D.Abbott, B.M.Gendall, A.R.Perugini, M.A.

(2021) Elife 10

  • DOI: https://doi.org/10.7554/eLife.69444
  • Primary Citation of Related Structures:  
    7MDS

  • PubMed Abstract: 

    Weeds are becoming increasingly resistant to our current herbicides, posing a significant threat to agricultural production. Therefore, new herbicides with novel modes of action are urgently needed. In this study, we exploited a novel herbicide target, dihydrodipicolinate synthase (DHDPS), which catalyses the first and rate-limiting step in lysine biosynthesis. The first class of plant DHDPS inhibitors with micromolar potency against Arabidopsis thaliana DHDPS was identified using a high-throughput chemical screen. We determined that this class of inhibitors binds to a novel and unexplored pocket within DHDPS, which is highly conserved across plant species. The inhibitors also attenuated the germination and growth of A. thaliana seedlings and confirmed their pre-emergence herbicidal activity in soil-grown plants. These results provide proof-of-concept that lysine biosynthesis represents a promising target for the development of herbicides with a novel mode of action to tackle the global rise of herbicide-resistant weeds.


  • Organizational Affiliation

    Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-hydroxy-tetrahydrodipicolinate synthase 1, chloroplastic
A, B
338Arabidopsis thalianaMutation(s): 0 
Gene Names: DHDPS1DHDPSDHPS1At3g60880T4C21_290
EC: 4.3.3.7
UniProt
Find proteins for Q9LZX6 (Arabidopsis thaliana)
Explore Q9LZX6 
Go to UniProtKB:  Q9LZX6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LZX6
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.29 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.183 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.47α = 90
b = 94.47β = 90
c = 181.41γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
Auto-Rickshawphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)AustraliaDP150103313
Australian Research Council (ARC)AustraliaDE190100806
National Health and Medical Research Council (NHMRC, Australia)AustraliaAPP1091976

Revision History  (Full details and data files)

  • Version 1.0: 2021-08-04
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description