8EY0

Structure of an orthogonal PYR1*:HAB1* chemical-induced dimerization module in complex with mandipropamid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.177 

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Ligand Structure Quality Assessment 


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Literature

An orthogonalized PYR1-based CID module with reprogrammable ligand-binding specificity.

Park, S.Y.Qiu, J.Wei, S.Peterson, F.C.Beltran, J.Medina-Cucurella, A.V.Vaidya, A.S.Xing, Z.Volkman, B.F.Nusinow, D.A.Whitehead, T.A.Wheeldon, I.Cutler, S.R.

(2024) Nat Chem Biol 20: 103-110

  • DOI: https://doi.org/10.1038/s41589-023-01447-7
  • Primary Citation of Related Structures:  
    8EY0

  • PubMed Abstract: 

    Plants sense abscisic acid (ABA) using chemical-induced dimerization (CID) modules, including the receptor PYR1 and HAB1, a phosphatase inhibited by ligand-activated PYR1. This system is unique because of the relative ease with which ligand recognition can be reprogrammed. To expand the PYR1 system, we designed an orthogonal '*' module, which harbors a dimer interface salt bridge; X-ray crystallographic, biochemical and in vivo analyses confirm its orthogonality. We used this module to create PYR1* MANDI /HAB1* and PYR1* AZIN /HAB1*, which possess nanomolar sensitivities to their activating ligands mandipropamid and azinphos-ethyl. Experiments in Arabidopsis thaliana and Saccharomyces cerevisiae demonstrate the sensitive detection of banned organophosphate contaminants using living biosensors and the construction of multi-input/output genetic circuits. Our new modules enable ligand-programmable multi-channel CID systems for plant and eukaryotic synthetic biology that can empower new plant-based and microbe-based sensing modalities.


  • Organizational Affiliation

    Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein phosphatase 2C 16A [auth B]333Arabidopsis thalianaMutation(s): 0 
Gene Names: HAB1P2C-HAAt1g72770F28P22.4
EC: 3.1.3.16
UniProt
Find proteins for Q9CAJ0 (Arabidopsis thaliana)
Explore Q9CAJ0 
Go to UniProtKB:  Q9CAJ0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9CAJ0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Abscisic acid receptor PYR1B [auth A]181Arabidopsis thalianaMutation(s): 0 
Gene Names: PYR1ABIP6RCAR11At4g17870T6K21.50
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
3UZ (Subject of Investigation/LOI)
Query on 3UZ

Download Ideal Coordinates CCD File 
E [auth A](2S)-2-(4-chlorophenyl)-N-{2-[3-methoxy-4-(prop-2-yn-1-yloxy)phenyl]ethyl}-2-(prop-2-yn-1-yloxy)ethanamide
C23 H22 Cl N O4
KWLVWJPJKJMCSH-QFIPXVFZSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.405α = 90
b = 92.214β = 90
c = 96.768γ = 90
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesNSF-2128016
National Science Foundation (NSF, United States)United States2128246

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-08
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Database references