9IX7 | pdb_00009ix7

Crystal structure of homolog of dihydroxyacid dehydratase(AstD) from Aspergillus terreus

• PDB DOI: https://doi.org/10.2210/pdb9IX7/pdb

• Classification: LYASE
• Organism(s): Aspergillus terreus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-26 Released: 2025-07-09 
• Deposition Author(s): Huang, W.X., Zhang, P.X., Zhou, J.H.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free: 
  0.232 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

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

• PubMed: 39494391 
• DOI: https://doi.org/10.34133/bdr.0046
• Primary Citation of Related Structures:  
  8HS0, 8IKZ, 8IMU, 9IX7, 9JPI, 9JSQ


• 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.

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Organizational Affiliation: 
• Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA, USA.
State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China.
Department of Molecular Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA.
Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095, USA.
Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California, Los Angeles, CA 90095, USA.
Department of Biological Chemistry, University of California, Los Angeles, CA 90095, USA.
School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly Evidence: fluorescence resonance energy transfer

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 120.68 kDa 
• Atom Count: 7,320 
• Modeled Residue Count: 928 
• Deposited Residue Count: 1,120 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
dihydroxy-acid dehydratase	A, B	560	Aspergillus terreus	Mutation(s): 0  Gene Names: ATEIFO6365_0004000400 EC: 4.2.1.9
UniProt
Find proteins for Q0CPG9 (Aspergillus terreus (strain NIH 2624 / FGSC A1156)) Explore Q0CPG9  Go to UniProtKB:  Q0CPG9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	C [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	D [auth A], E [auth B], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.29 Å
• R-Value Free:  0.232 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.614	α = 90
b = 66.278	β = 90
c = 268.953	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
PHASES	phasing
HKL-3000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-07-09 
Deposition Author(s): Huang, W.X., Zhang, P.X., Zhou, J.H.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32071446

Revision History  

• Version 1.0: 2025-07-09
  Type: Initial release