5YWG

Crystal structure of Arabidopsis thaliana HPPD complexed with Mesotrione


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.603 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.262 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular insights into the mechanism of 4-hydroxyphenylpyruvate dioxygenase inhibition: enzyme kinetics, X-ray crystallography and computational simulations.

Lin, H.Y.Yang, J.F.Wang, D.W.Hao, G.F.Dong, J.Q.Wang, Y.X.Yang, W.C.Wu, J.W.Zhan, C.G.Yang, G.F.

(2019) FEBS J. 286: 975-990

  • DOI: 10.1111/febs.14747
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Slow-binding inhibitors with long residence time on the target often display superior efficacy in vivo. Rationally designing inhibitors with low off-target rates is restricted by a limited understanding of the structural basis of slow-binding inhibit ...

    Slow-binding inhibitors with long residence time on the target often display superior efficacy in vivo. Rationally designing inhibitors with low off-target rates is restricted by a limited understanding of the structural basis of slow-binding inhibition kinetics in enzyme-drug interactions. 4-Hydroxyphenylpyruvate dioxygenase (HPPD) is an important target for drug and herbicide development. Although the time-dependent behavior of HPPD inhibitors has been studied for decades, its structural basis and mechanism remain unclear. Herein, we report a detailed experimental and computational study that explores structures for illustrating the slow-binding inhibition kinetics of HPPD. We observed the conformational change of Phe428 at the C-terminal α-helix in the inhibitor-bound structures and further identified that the inhibition kinetics of drugs are related to steric hindrance of Phe428. These detailed structural and mechanistic insights illustrate that steric hindrance is highly associated with the time-dependent behavior of HPPD inhibitors. These findings may enable rational design of new potent HPPD-targeted drugs or herbicides with longer target residence time and improved properties. DATABASE: Structure data are available in the PDB under the accession numbers 5CTO (released), 5DHW (released), and 5YWG (released).


    Organizational Affiliation

    Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, Chemical Biology Center, College of Chemistry, Central China Normal University, Wuhan, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
4-hydroxyphenylpyruvate dioxygenase
A, B
445Arabidopsis thalianaMutation(s): 0 
Gene Names: HPD (PDS1)
EC: 1.13.11.27
Find proteins for P93836 (Arabidopsis thaliana)
Go to Gene View: HPD
Go to UniProtKB:  P93836
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
92L
Query on 92L

Download SDF File 
Download CCD File 
A, B
2-[(4-methylsulfonyl-2-nitro-phenyl)-oxidanyl-methylidene]cyclohexane-1,3-dione
Mesotrione
C14 H13 N O7 S
PILIZHLSOWYJPQ-UHFFFAOYSA-N
 Ligand Interaction
CO
Query on CO

Download SDF File 
Download CCD File 
A, B
COBALT (II) ION
Co
XLJKHNWPARRRJB-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.603 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.262 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 95.719α = 90.00
b = 95.719β = 90.00
c = 195.170γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-11-29 
  • Released Date: 2019-01-16 
  • Deposition Author(s): Lin, H.Y., Yang, W.C.

Funding OrganizationLocationGrant Number
National Science Foundation (China)China21672079

Revision History 

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-02-06
    Type: Data collection, Database references
  • Version 1.2: 2019-03-20
    Type: Data collection, Database references