9JPI

The complex structure of DHAD with aspterric acid (AA).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 
    0.214 (Depositor), 0.214 (DCC) 
  • R-Value Work: 
    0.182 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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Literature

Structural Bases of Dihydroxy Acid Dehydratase Inhibition and Biodesign for Self-Resistance.

Zang, X.Bat-Erdene, U.Huang, W.Wu, Z.Jacobsen, S.E.Tang, Y.Zhou, J.

(2024) Biodes Res 6: 0046-0046

  • DOI: https://doi.org/10.34133/bdr.0046
  • Primary Citation of Related Structures:  
    8HS0, 8IKZ, 8IMU, 9JPI

  • PubMed Abstract: 

    Dihydroxy acid dehydratase (DHAD) is the third enzyme in the plant branched-chain amino acid biosynthetic pathway and the target for commercial herbicide development. We have previously reported the discovery of fungal natural product aspterric acid (AA) as a submicromolar inhibitor of DHAD through self-resistance gene directed genome mining. Here, we reveal the mechanism of AA inhibition on DHAD and the self-resistance mechanism of AstD, which is encoded by the self-resistance gene ast D. As a competitive inhibitor, the hydroxycarboxylic acid group of AA mimics the binding of the natural substrate of DHAD, while the hydrophobic moiety of AA occupies the substrate entrance cavity. Compared to DHAD, AstD has a relatively narrow substrate channel to prevent AA from binding. Several mutants of DHAD were generated and assayed to validate the self-resistance mechanism and to confer Arabidopsis thaliana DHAD with AA resistance. These results will lead to the engineering of new type of herbicides targeting DHAD and provide direction for the ecological construction of herbicide-resistant crops.


  • Organizational Affiliation

    Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dihydroxy-acid dehydratase, chloroplastic580Arabidopsis thalianaMutation(s): 2 
Gene Names: DHADAt3g23940F14O13.13
EC: 4.2.1.9
UniProt
Find proteins for Q9LIR4 (Arabidopsis thaliana)
Explore Q9LIR4 
Go to UniProtKB:  Q9LIR4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LIR4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K0O (Subject of Investigation/LOI)
Query on K0O

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
Aspterric Acid
C15 H22 O4
IOYVXXQKVQKQIG-CTHBEMJXSA-N
FES
Query on FES

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

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free:  0.214 (Depositor), 0.214 (DCC) 
  • R-Value Work:  0.182 (Depositor), 0.182 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.89α = 90
b = 135.89β = 90
c = 66.64γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release