7VKA

Crystal Structure of GH3.6 in complex with an inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 

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This is version 1.2 of the entry. See complete history


Literature

Chemical genetic screening identifies nalacin as an inhibitor of GH3 amido synthetase for auxin conjugation.

Xie, Y.Zhu, Y.Wang, N.Luo, M.Ota, T.Guo, R.Takahashi, I.Yu, Z.Aizezi, Y.Zhang, L.Yan, Y.Zhang, Y.Bao, H.Wang, Y.Zhu, Z.Huang, A.C.Zhao, Y.Asami, T.Huang, H.Guo, H.Jiang, K.

(2022) Proc Natl Acad Sci U S A 119: e2209256119-e2209256119

  • DOI: https://doi.org/10.1073/pnas.2209256119
  • Primary Citation of Related Structures:  
    7VKA

  • PubMed Abstract: 

    Auxin inactivation is critical for plant growth and development. To develop plant growth regulators functioning in auxin inactivation pathway, we performed a phenotype-based chemical screen in Arabidopsis and identified a chemical, nalacin, that partially mimicked the effects of auxin. Genetic, pharmacological, and biochemical approaches demonstrated that nalacin exerts its auxin-like activities by inhibiting indole-3-acetic acid (IAA) conjugation that is mediated by Gretchen Hagen 3 (GH3) acyl acid amido synthetases. The crystal structure of Arabidopsis GH3.6 in complex with D4 (a derivative of nalacin) together with docking simulation analysis revealed the molecular basis of the inhibition of group II GH3 by nalacin. Sequence alignment analysis indicated broad bioactivities of nalacin and D4 as inhibitors of GH3s in vascular plants, which were confirmed, at least, in tomato and rice. In summary, our work identifies nalacin as a potent inhibitor of IAA conjugation mediated by group II GH3 that plays versatile roles in hormone-regulated plant development and has potential applications in both basic research and agriculture.


  • Organizational Affiliation

    Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Indole-3-acetic acid-amido synthetase GH3.6
A, B
613Arabidopsis thalianaMutation(s): 0 
Gene Names: GH3.6DFL1At5g54510F24B18.13
EC: 6.3.2
UniProt
Find proteins for Q9LSQ4 (Arabidopsis thaliana)
Explore Q9LSQ4 
Go to UniProtKB:  Q9LSQ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9LSQ4
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.175 
  • Space Group: P 64
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 205.871α = 90
b = 205.871β = 90
c = 65.665γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChinaKQTD20190929173906742

Revision History  (Full details and data files)

  • Version 1.0: 2022-08-31
    Type: Initial release
  • Version 1.1: 2023-03-15
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description