7Z1R

X-ray crystal structure of SLPYL1-E151D mutant ABA complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure-Based Modulation of the Ligand Sensitivity of a Tomato Dimeric Abscisic Acid Receptor Through a Glu to Asp Mutation in the Latch Loop.

Infantes, L.Rivera-Moreno, M.Daniel-Mozo, M.Benavente, J.L.Ocana-Cuesta, J.Coego, A.Lozano-Juste, J.Rodriguez, P.L.Albert, A.

(2022) Front Plant Sci 13: 884029-884029

  • DOI: https://doi.org/10.3389/fpls.2022.884029
  • Primary Citation of Related Structures:  
    7Z1P, 7Z1Q, 7Z1R, 7Z1S

  • PubMed Abstract: 

    The binding of the plant phytohormone Abscisic acid (ABA) to the family of ABA receptors (PYR/PYL/RCAR) triggers plant responses to abiotic stress. Thus, the implementation of genetic or chemical strategies to modulate PYR/PYL activity might be biotechnologically relevant. We have employed the available structural information on the PYR/PYL receptors to design SlPYL1, a tomato receptor, harboring a single point mutation that displays enhanced ABA dependent and independent activity. Interestingly, crystallographic studies show that this mutation is not directly involved in ABA recognition or in the downstream phosphatase (PP2C) inhibitory interaction, rather, molecular dynamic based ensemble refinement restrained by crystallographic data indicates that it enhances the conformational variability required for receptor activation and it is involved in the stabilization of an active form of the receptor. Moreover, structural studies on this receptor have led to the identification of niacin as an ABA antagonist molecule in vivo . We have found that niacin blocks the ABA binding site by mimicking ABA receptor interactions, and the niacin interaction inhibits the biochemical activity of the receptor.


  • Organizational Affiliation

    Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Científicas, Madrid, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SlPYL1-E151D ABAA [auth D000]232Solanum lycopersicumMutation(s): 1 
Gene Names: 101268417
UniProt
Find proteins for A0A3Q7HTY9 (Solanum lycopersicum)
Explore A0A3Q7HTY9 
Go to UniProtKB:  A0A3Q7HTY9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3Q7HTY9
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.808α = 90
b = 87.808β = 90
c = 55.184γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
XDSdata scaling
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2020-119805RB-I00

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description