7K38

Crystal structure of Pisum sativum KAI2 in complex with GR24-ent5DS product


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.173 

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This is version 1.3 of the entry. See complete history


Literature

Structural and functional analyses explain Pea KAI2 receptor diversity and reveal stereoselective catalysis during signal perception.

Guercio, A.M.Torabi, S.Cornu, D.Dalmais, M.Bendahmane, A.Le Signor, C.Pillot, J.P.Le Bris, P.Boyer, F.D.Rameau, C.Gutjahr, C.de Saint Germain, A.Shabek, N.

(2022) Commun Biol 5: 126-126

  • DOI: https://doi.org/10.1038/s42003-022-03085-6
  • Primary Citation of Related Structures:  
    7K2Z, 7K38

  • PubMed Abstract: 

    KAI2 proteins are plant α/β hydrolase receptors which perceive smoke-derived butenolide signals and endogenous, yet unidentified KAI2-ligands (KLs). The number of functional KAI2 receptors varies among species and KAI2 gene duplication and sub-functionalization likely plays an adaptative role by altering specificity towards different KLs. Legumes represent one of the largest families of flowering plants and contain many agronomic crops. Prior to their diversification, KAI2 underwent duplication resulting in KAI2A and KAI2B. Here we demonstrate that Pisum sativum KAI2A and KAI2B are active receptors and enzymes with divergent ligand stereoselectivity. KAI2B has a higher affinity for and hydrolyses a broader range of substrates including strigolactone-like stereoisomers. We determine the crystal structures of PsKAI2B in apo and butenolide-bound states. The biochemical, structural, and mass spectra analyses of KAI2s reveal a transient intermediate on the catalytic serine and a stable adduct on the catalytic histidine, confirming its role as a bona fide enzyme. Our work uncovers the stereoselectivity of ligand perception and catalysis by diverged KAI2 receptors and proposes adaptive sensitivity to KAR/KL and strigolactones by KAI2B.


  • Organizational Affiliation

    Department of Plant Biology, College of Biological Sciences, University of California, Davis, CA, 95616, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PsKAI2B protein270Pisum sativumMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VTY (Subject of Investigation/LOI)
Query on VTY

Download Ideal Coordinates CCD File 
B [auth A](5S)-5-hydroxy-3-methylfuran-2(5H)-one
C5 H6 O3
HQIZYPQNJWENRT-BYPYZUCNSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.089α = 90
b = 71.82β = 117.3
c = 48.794γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-02-16
    Type: Initial release
  • Version 1.1: 2022-02-23
    Changes: Database references
  • Version 1.2: 2022-03-02
    Changes: Database references
  • Version 1.3: 2023-10-18
    Changes: Data collection, Refinement description