3WG8

Crystal structure of the abscisic acid receptor PYR1 in complex with an antagonist AS6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Designed abscisic acid analogs as antagonists of PYL-PP2C receptor interactions

Takeuchi, J.Okamoto, M.Akiyama, T.Muto, T.Yajima, S.Sue, M.Seo, M.Kanno, Y.Kamo, T.Endo, A.Nambara, E.Hirai, N.Ohnishi, T.Cutler, S.R.Todoroki, Y.

(2014) Nat Chem Biol 10: 477-482

  • DOI: https://doi.org/10.1038/nchembio.1524
  • Primary Citation of Related Structures:  
    3WG8

  • PubMed Abstract: 

    The plant stress hormone abscisic acid (ABA) is critical for several abiotic stress responses. ABA signaling is normally repressed by group-A protein phosphatases 2C (PP2Cs), but stress-induced ABA binds Arabidopsis PYR/PYL/RCAR (PYL) receptors, which then bind and inhibit PP2Cs. X-ray structures of several receptor-ABA complexes revealed a tunnel above ABA's 3' ring CH that opens at the PP2C binding interface. Here, ABA analogs with sufficiently long 3' alkyl chains were predicted to traverse this tunnel and block PYL-PP2C interactions. To test this, a series of 3'-alkylsulfanyl ABAs were synthesized with different alkyl chain lengths. Physiological, biochemical and structural analyses revealed that a six-carbon alkyl substitution produced a potent ABA antagonist that was sufficiently active to block multiple stress-induced ABA responses in vivo. This study provides a new approach for the design of ABA analogs, and the results validated structure-based design for this target class.


  • Organizational Affiliation

    1] Graduate School of Science and Technology, Shizuoka University, Shizuoka, Japan. [2].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Abscisic acid receptor PYR1227Arabidopsis thalianaMutation(s): 0 
Gene Names: PYR1
UniProt
Find proteins for O49686 (Arabidopsis thaliana)
Explore O49686 
Go to UniProtKB:  O49686
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO49686
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6AS
Query on 6AS

Download Ideal Coordinates CCD File 
B [auth A](2Z,4E)-5-[(1S)-3-(hexylsulfanyl)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
C21 H32 O4 S
AOFXVHRNNSAVEA-IHZHKDPYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.239 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.932α = 90
b = 66.932β = 90
c = 78.237γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-07
    Type: Initial release
  • Version 1.1: 2014-06-11
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description