5ZE4

The structure of holo- structure of DHAD complex with [2Fe-2S] cluster


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Resistance-gene-directed discovery of a natural-product herbicide with a new mode of action.

Yan, Y.Liu, Q.Zang, X.Yuan, S.Bat-Erdene, U.Nguyen, C.Gan, J.Zhou, J.Jacobsen, S.E.Tang, Y.

(2018) Nature 559: 415-418

  • DOI: 10.1038/s41586-018-0319-4
  • Primary Citation of Related Structures:  
    5ZE4

  • PubMed Abstract: 
  • Bioactive natural products have evolved to inhibit specific cellular targets and have served as lead molecules for health and agricultural applications for the past century 1-3 . The post-genomics era has brought a renaissance in the discovery of natural products using synthetic-biology tools 4-6 ...

    Bioactive natural products have evolved to inhibit specific cellular targets and have served as lead molecules for health and agricultural applications for the past century 1-3 . The post-genomics era has brought a renaissance in the discovery of natural products using synthetic-biology tools 4-6 . However, compared to traditional bioactivity-guided approaches, genome mining of natural products with specific and potent biological activities remains challenging 4 . Here we present the discovery and validation of a potent herbicide that targets a critical metabolic enzyme that is required for plant survival. Our approach is based on the co-clustering of a self-resistance gene in the natural-product biosynthesis gene cluster 7-9 , which provides insight into the potential biological activity of the encoded compound. We targeted dihydroxy-acid dehydratase in the branched-chain amino acid biosynthetic pathway in plants; the last step in this pathway is often targeted for herbicide development 10 . We show that the fungal sesquiterpenoid aspterric acid, which was discovered using the method described above, is a sub-micromolar inhibitor of dihydroxy-acid dehydratase that is effective as a herbicide in spray applications. The self-resistance gene astD was validated to be insensitive to aspterric acid and was deployed as a transgene in the establishment of plants that are resistant to aspterric acid. This herbicide-resistance gene combination complements the urgent ongoing efforts to overcome weed resistance 11 . Our discovery demonstrates the potential of using a resistance-gene-directed approach in the discovery of bioactive natural products.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA, USA. yitang@ucla.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Dihydroxy-acid dehydratase, chloroplasticA573Arabidopsis thalianaMutation(s): 2 
Gene Names: DHADILVDAt3g23940F14O13.13
EC: 4.2.1.9
UniProt
Find proteins for Q9LIR4 (Arabidopsis thaliana)
Explore Q9LIR4 
Go to UniProtKB:  Q9LIR4
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FES
Query on FES

Download Ideal Coordinates CCD File 
B [auth A]FE2/S2 (INORGANIC) CLUSTER
Fe2 S2
NIXDOXVAJZFRNF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
F [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.175 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.467α = 90
b = 135.467β = 90
c = 65.978γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 1.1: 2018-08-01
    Changes: Data collection, Database references