3W9R

Crystal structure of the high-affinity abscisic acid receptor PYL9/RCAR9 bound to ABA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Mechanism of high-affinity abscisic acid binding to PYL9/RCAR1

Nakagawa, M.Kagiyama, M.Shibata, N.Hirano, Y.Hakoshima, T.

(2014) Genes Cells --: --

  • DOI: 10.1111/gtc.12140

  • PubMed Abstract: 
  • Arabidopsis receptors of abscisic acid (ABA), the key plant hormone for adaptation to water stress, comprise 14 PYR/PYLs/RCARs proteins classified into three subfamilies I, II, and III, which suggests functional differentiation. Although their monome ...

    Arabidopsis receptors of abscisic acid (ABA), the key plant hormone for adaptation to water stress, comprise 14 PYR/PYLs/RCARs proteins classified into three subfamilies I, II, and III, which suggests functional differentiation. Although their monomer-dimer equilibria may be correlated with differences in their ABA-binding affinities, how the dimerization decreases the affinity is unclear. Comparative structural and binding studies between PYL9, which is a representative of high-affinity subfamily I, and low-affinity members of subfamily III reveals that the nonpolar triplet (Ile110, Val162, and Leu165) and Pro64 contribute to enhance ABA-binding affinity by inducing a shift of the ABA carboxyl group to form additional direct hydrogen bonds with conserved Asn169. Our mutation studies of PYL1 successfully produced a monomeric mutant PYL1 exhibiting low ABA affinity and also a dimeric mutant PYL1 exhibiting high ABA-binding affinity, suggesting that dimer formation of ABA receptors is not essential for their low ABA-binding affinity. Our study contributes toward establishing the structural basis for the higher ABA-binding affinity of the subfamily receptors and provides a clue for understanding the broad spectrum of hormone actions in plants manifested by the different hormone-binding affinity of multiple receptors.


    Organizational Affiliation

    Structural Biology Laboratory, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara, 630-0192, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Abscisic acid receptor PYL9
A
189Arabidopsis thalianaMutation(s): 0 
Gene Names: PYL9 (RCAR1)
Find proteins for Q84MC7 (Arabidopsis thaliana)
Go to UniProtKB:  Q84MC7
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
A8S
Query on A8S

Download SDF File 
Download CCD File 
A
(2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxocyclohex-2-en-1-yl]-3-methylpenta-2,4-dienoic acid
(+)-abscisic acid, (2Z,4E)-5-[(1S)-1-hydroxy-2,6,6-trimethyl-4-oxo-2-cyclohexen-1-yl]-3-methyl-2,4-pentadienoic acid
C15 H20 O4
JLIDBLDQVAYHNE-YKALOCIXSA-N
 Ligand Interaction
P6G
Query on P6G

Download SDF File 
Download CCD File 
A
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
A8SKd: 660 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.188 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 111.405α = 90.00
b = 111.405β = 90.00
c = 40.478γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-09
    Type: Initial release