7K2Z | pdb_00007k2z

Crystal structure of Pisum sativum KAI2 Apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free: 
    0.180 (Depositor), 0.179 (DCC) 
  • R-Value Work: 
    0.156 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 
    0.157 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7K2Z

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 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.

Macromolecule Content 

  • Total Structure Weight: 30.14 kDa 
  • Atom Count: 2,395 
  • Modeled Residue Count: 270 
  • Deposited Residue Count: 270 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
PsKAI2B protein270Lathyrus oleraceusMutation(s): 0 
UniProt
Find proteins for A0A8X6EGX8 (Pisum sativum)
Explore A0A8X6EGX8 
Go to UniProtKB:  A0A8X6EGX8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8X6EGX8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL

Query on GOL



Download:Ideal Coordinates CCD File
B [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.61 Å
  • R-Value Free:  0.180 (Depositor), 0.179 (DCC) 
  • R-Value Work:  0.156 (Depositor), 0.160 (DCC) 
  • R-Value Observed: 0.157 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 87.595α = 90
b = 71.146β = 117.62
c = 49.065γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



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