8VD1

Crystal Structure of KAI2 from Oryza sativa with MPD


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into rice KAI2 receptor provide functional implications for perception and signal transduction.

Guercio, A.M.Gilio, A.K.Pawlak, J.Shabek, N.

(2024) J Biol Chem 300: 107593-107593

  • DOI: https://doi.org/10.1016/j.jbc.2024.107593
  • Primary Citation of Related Structures:  
    8VCZ, 8VD1, 8VD3

  • PubMed Abstract: 

    KAI2 receptors, classified as plant α/β hydrolase enzymes, are capable of perceiving smoke-derived butenolide signals and endogenous, yet unidentified KAI2-ligands (KLs). While the number of functional KAI2 receptors varies among land plant species, rice has only one KAI2 gene. Rice, a significant crop and representative of grasses, relies on KAI2-mediated Arbuscular mycorrhiza (AM) symbioses to flourish in traditionally arid and nutrient-poor environments. This study presents the first crystal structure of an active rice (Oryza sativa, Os) KAI2 hydrolase receptor. Our structural and biochemical analyses uncover grass-unique pocket residues influencing ligand sensitivity and hydrolytic activity. Through structure-guided analysis, we identify a specific residue whose mutation enables the increase or decrease of ligand perception, catalytic activity, and signal transduction. Furthermore, we investigate OsKAI2-mediated signaling by examining its ability to form a complex with its binding partner, the F-box protein DWARF3 (D3) ubiquitin ligase and subsequent degradation of the target substrate OsSMAX1, demonstrating the significant role of hydrophobic interactions in the OsKAI2-D3 interface. This study provides new insights into the diverse and pivotal roles of the OsKAI2 signaling pathway in the plant kingdom, particularly in grasses.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable esterase D14L272Oryza sativaMutation(s): 0 
Gene Names: D14LOs03g0437600LOC_Os03g32270Os11g0384789
UniProt
Find proteins for Q10J20 (Oryza sativa subsp. japonica)
Explore Q10J20 
Go to UniProtKB:  Q10J20
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ10J20
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MPD
Query on MPD

Download Ideal Coordinates CCD File 
B [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.29 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.153 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.711α = 90
b = 86.477β = 114.94
c = 44.617γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-31
    Type: Initial release
  • Version 1.1: 2024-08-07
    Changes: Database references
  • Version 1.2: 2024-08-21
    Changes: Database references