9KGM | pdb_00009kgm

Complex structure of OsHPPD with MBQ

• PDB DOI: https://doi.org/10.2210/pdb9KGM/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Oryza sativa Japonica Group
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-11-08 Released: 2025-11-12 
• Deposition Author(s): Yang, G.-F., Lin, H.-Y., Dong, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 
  0.292 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.276 (Depositor), 0.275 (DCC) 
• R-Value Observed: 
  0.277 (Depositor) 

Starting Model: experimental

Literature

Structure-Based Directed Evolution of Rice 4-Hydroxyphenylpyruvate Dioxygenase Confers Enhanced Herbicide Tolerance.

Dong, J., Dong, J., Wang, X.L., Wei, X.F., Yang, G.F., Lin, H.Y.

(2025) J Agric Food Chem 73: 18923-18931

• PubMed: 40668751 
• DOI: https://doi.org/10.1021/acs.jafc.5c06678
• Primary Citation Related Structures: 
  9KGM


• PubMed Abstract: 
  

  Precise gene modification is pivotal in molecular breeding. 4-Hydroxyphenylpyruvate dioxygenase (HPPD) plays a crucial role in the development of herbicide-resistant crops. But how to modify HPPD and thereby confer herbicide resistance in plants remains unclear. This research delineates the structure of Oryza sativa HPPD ( Os HPPD) complexed with Methyl-Benquitrione (MBQ) and identifies potential residues that confer herbicide resistance. Enzymatic tests of the C-terminal α9 helix variants showed that K418D, E423Q, E423M, E423S, E423T, E423L, E423W, E432I, E432M, E432W, and E432F demonstrated preserved catalytic efficiency. The herbicide resistance test displayed that K418D, E423Q, E423M, E432I, and E432M acquired 1.5- to 3-fold enhancements against mesotrione, topramezone, MBQ, and A1 in vitro. Especially, the forced expression of E432M in Arabidopsis thaliana significantly elevated herbicide resistance compared to the wild type. These findings highlight the potential of specific Os HPPD modifications in developing crops with enhanced herbicide resistance, providing a foundation for future genetic engineering strategies.

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Organizational Affiliation: 
• State Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, PR China.
International Joint Research Center for Intelligent Biosensor Technology and Health, Central China Normal University, Wuhan 430079, PR China.
Hubei Shizhen Laboratory, Wuhan 430061, PR China.
School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, PR China.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 94.93 kDa 
• Atom Count: 5,571 
• Modeled Residue Count: 765 
• Deposited Residue Count: 892 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
4-hydroxyphenylpyruvate dioxygenase	A, B	446	Oryza sativa Japonica Group	Mutation(s): 0  Gene Names: OSJNBa0085K21.52, P0669G09.6
UniProt
Find proteins for Q6H4V1 (Oryza sativa subsp. japonica) Explore Q6H4V1  Go to UniProtKB:  Q6H4V1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
92X	D [auth A], F [auth B]	1,5-dimethyl-3-(2-methylphenyl)-6-(2-oxidanyl-6-oxidanylidene-cyclohexen-1-yl)carbonyl-quinazoline-2,4-dione C24 H22 N2 O5 ZGLNNDUJJLHJTE-UHFFFAOYSA-N
CO	C [auth A], E [auth B]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free:  0.292 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.276 (Depositor), 0.275 (DCC) 
• R-Value Observed: 0.277 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 153.676	α = 90
b = 153.676	β = 90
c = 81.588	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-12 
Deposition Author(s): Yang, G.-F., Lin, H.-Y., Dong, J.

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

Revision History  

• Version 1.0: 2025-11-12
  Type: Initial release
  
• Version 1.1: 2026-04-22
  Changes: Database references