5ZCL

Crystal structure of OsPP2C50 I267L:OsPYL/RCAR3 with (+)-ABA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Comprehensive survey of the VxG Phi L motif of PP2Cs from Oryza sativa reveals the critical role of the fourth position in regulation of ABA responsiveness.

Han, S.Lee, J.Y.Lee, Y.Kim, T.H.Lee, S.

(2019) Plant Mol Biol 101: 455-469

  • DOI: https://doi.org/10.1007/s11103-019-00916-9
  • Primary Citation of Related Structures:  
    5ZCG, 5ZCH, 5ZCL

  • PubMed Abstract: 

    Regulation of abscisic acid (ABA) signaling is crucial in balancing responses to abiotic stresses and retaining growth in planta. An ABA receptor (PYL/RCAR) and a protein phosphatase (PP2C), a co-receptor, form a complex upon binding to ABA. Previously we reported that the second and fourth positions in the VxGΦL motif of PP2Cs from Oryza sativa are critical in the interaction of PP2Cs with PYL/RCARs. Considering substantial effects of the VxGΦL motif on ABA signaling outputs, further comprehensive characterization of residues in the second and fourth positions are required. Here we surveyed the second and fourth positions of the VxGΦL motif by combination of biochemical, structural and physiological analyses. We found that the fourth position of the VxGΦL motif, highly conserved to small hydrophobic residues, was a key determinant of the OsPP2C50:OsPYL/RCAR interactions across subfamilies. Large hydrophobic or any hydrophilic residues in the fourth position abrogated ABA responsiveness. Analysis of crystal structures of OsPP2C50 mutants, S265L/I267V ("LV"), I267L ("SL") and I267W ("SW"), in complex with ABA and OsPYL/RCAR3, along with energy calculation of the complexes, uncovered that a bulky hydrophobic residue in the fourth position of the VxGΦL motif pushed away side chains of nearby residues, conferring side-chain rotameric energy stress. Hydrophilic residues in this position imposed solvation energy stress to the PP2C:PYL/RCAR complex. Germination and gene expression analyses corroborated that OsPP2C50 AS and AK mutants modulated ABA responsiveness in Arabidopsis. Our results suggest that ABA responsiveness could be fine-tuned by the fourth position of the VxGΦL motif on PP2Cs. KEY MESSAGE: We comprehensively surveyed the VxGΦL motif to find that the fourth position, highly conserved to small hydrophobic residues, was critical in regulating ABA responsiveness.


  • Organizational Affiliation

    Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Republic of Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable protein phosphatase 2C 50A,
C [auth B]
328Oryza sativa Japonica GroupMutation(s): 4 
Gene Names: Os05g0537400LOC_Os05g46040OJ1741_B01.18OSJNBa0052K01.2
EC: 3.1.3.16
UniProt
Find proteins for Q6L5H6 (Oryza sativa subsp. japonica)
Explore Q6L5H6 
Go to UniProtKB:  Q6L5H6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6L5H6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ABA receptor RCAR3B [auth C],
D
175Oryza sativaMutation(s): 0 
UniProt
Find proteins for Q6EN42 (Oryza sativa subsp. japonica)
Explore Q6EN42 
Go to UniProtKB:  Q6EN42
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6EN42
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.66 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.096α = 90
b = 130.262β = 115.99
c = 80.252γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
the Rural Development AgencyKorea, Republic OfPJ013676
the National Research Foundation of KoreaKorea, Republic OfNRF-2017R1D1A1B03032185
the National Research Foundation of KoreaKorea, Republic OfSRC-2017R1A5A1014560

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-06
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references, Derived calculations
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.3: 2024-10-09
    Changes: Structure summary