8EY0 | pdb_00008ey0

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

• PDB DOI: https://doi.org/10.2210/pdb8EY0/pdb

• Classification: PLANT PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-10-26 Released: 2023-11-08 
• Deposition Author(s): Park, S.-Y., Volkman, B.F., Cutler, S.R., Peterson, F.C.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.234 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

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

• PubMed: 37872402 
• DOI: https://doi.org/10.1038/s41589-023-01447-7
• Primary Citation 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.

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Organizational Affiliation: 
• Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA.
Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA.
Department of Biochemistry, University of California, Riverside, Riverside, CA, USA.
Department of Biochemistry, Medical College of Wisconsin, Milwaukee, WI, USA.
Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA.
Donald Danforth Plant Science Center, St. Louis, MO, USA.
Department of Chemical and Biological Engineering, University of Colorado, Boulder, CO, USA.
Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA. [e-mail].
Department of Chemical and Environmental Engineering, University of California, Riverside, Riverside, CA, USA. [e-mail].
Center for Industrial Biotechnology, University of California, Riverside, Riverside, CA, USA. [e-mail].
Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA, USA. [e-mail].
Institute for Integrative Genome Biology, University of California, Riverside, Riverside, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 58.11 kDa 
• Atom Count: 3,827 
• Modeled Residue Count: 468 
• Deposited Residue Count: 514 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein phosphatase 2C 16	A [auth B]	333	Arabidopsis thaliana	Mutation(s): 0  Gene Names: HAB1, P2C-HA, At1g72770, F28P22.4 EC: 3.1.3.16
UniProt
Find proteins for Q9CAJ0 (Arabidopsis thaliana) Explore Q9CAJ0  Go to UniProtKB:  Q9CAJ0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Abscisic acid receptor PYR1	B [auth A]	181	Arabidopsis thaliana	Mutation(s): 0  Gene Names: PYR1, ABIP6, RCAR11, At4g17870, T6K21.50
UniProt
Find proteins for O49686 (Arabidopsis thaliana) Explore O49686  Go to UniProtKB:  O49686

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3UZ (Subject of Investigation/LOI)	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	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 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.405	α = 90
b = 92.214	β = 90
c = 96.768	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-11-08 
Deposition Author(s): Park, S.-Y., Volkman, B.F., Cutler, S.R., Peterson, F.C.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	NSF-2128016
National Science Foundation (NSF, United States)	United States	2128246

Revision History  

• Version 1.0: 2023-11-08
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Database references
• Version 1.2: 2026-03-04
  Changes: Refinement description, Structure summary