3NEF

High-resolution pyrabactin-bound PYL1 structure


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Functional mechanism of the ABA agonist pyrabactin

Hao, Q.Yin, P.Yan, C.Yuan, X.Li, W.Zhang, Z.Liu, L.Wang, J.Yan, N.

(2010) J.Biol.Chem. 285: 28946-28952

  • DOI: 10.1074/jbc.M110.149005
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Pyrabactin is a synthetic abscisic acid (ABA) agonist that selectively inhibits seed germination. The use of pyrabactin was pivotal in the identification of the PYR1/PYL/RCAR family (PYL) of proteins as the ABA receptor. Although they both act throug ...

    Pyrabactin is a synthetic abscisic acid (ABA) agonist that selectively inhibits seed germination. The use of pyrabactin was pivotal in the identification of the PYR1/PYL/RCAR family (PYL) of proteins as the ABA receptor. Although they both act through PYL proteins, pyrabactin and ABA share no apparent chemical or structural similarity. It remains unclear how pyrabactin functions as an ABA agonist. Here, we report the crystal structure of pyrabactin in complex with PYL1 at 2.4 A resolution. Structural and biochemical analyses revealed that recognition of pyrabactin by the pocket residues precedes the closure of switch loop CL2. Structural comparison between pyrabactin- and ABA-bound PYL1 reveals a general principle in the arrangements of function groups of the two distinct ligands. The study provides a framework for the development of novel ABA agonists that may have applicable potentials in agriculture.


    Organizational Affiliation

    State Key Laboratory of Biomembrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Abscisic acid receptor PYL1
A, B
202Arabidopsis thalianaMutation(s): 0 
Gene Names: PYL1 (RCAR12)
Find proteins for Q8VZS8 (Arabidopsis thaliana)
Go to UniProtKB:  Q8VZS8
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PYV
Query on PYV

Download SDF File 
Download CCD File 
A
4-bromo-N-(pyridin-2-ylmethyl)naphthalene-1-sulfonamide
Pyrabactin
C16 H13 Br N2 O2 S
GJSDYQXOSHKOGX-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PYVIC50: 1140 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.223 
  • R-Value Work: 0.188 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 128.570α = 90.00
b = 128.570β = 90.00
c = 87.240γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
PHASERphasing
BSSdata collection
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-06-08 
  • Released Date: 2010-06-16 
  • Deposition Author(s): Yan, N.

Revision History 

  • Version 1.0: 2010-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance