8QCW

The crystal structure of the truncated form of Lotus japonicus kinase 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.250 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Biochemical and Structural Studies of LjSK1, a Lotus japonicus GSK3 beta /SHAGGY-like Kinase, Reveal Its Functional Role.

Solovou, T.G.A.Stravodimos, G.Papadopoulos, G.E.Skamnaki, V.T.Papadopoulou, K.Leonidas, D.D.

(2024) J Agric Food Chem 72: 3763-3772

  • DOI: https://doi.org/10.1021/acs.jafc.3c07101
  • Primary Citation of Related Structures:  
    8QCW

  • PubMed Abstract: 

    The crystal structure of a truncated form of the Lotus japonicus glycogen synthase kinase 3β (GSK3β) like kinase (LjSK1 90-467 ) has been resolved at 2.9 Å resolution, providing, for the first time, structural data for a plant GKS3β like kinase. The 3D structure of LjSK1 90-467 revealed conservation at the structural level for this plant member of the GSK3β family. However, comparative structural analysis to the human homologue revealed significant differences at the N- and C-termini, supporting the notion for an additional regulatory mechanism in plant GSK3-like kinases. Structural similarities at the catalytic site and the ATP binding site explained the similarity in the function of the human and plant protein. LjSK1 and lupeol are strongly linked to symbiotic bacterial infection and nodulation initiation. An inhibitory capacity of lupeol (IC 50 = 0.77 μM) for LjSK1 was discovered, providing a biochemical explanation for the involvement of these two molecules in nodule formation, and constituted LjSK1 as a molecular target for the discovery of small molecule modulators for crop protection and development. Studies on the inhibitory capacity of two phytogenic triterpenoids (betulinic acid and hederacoside C) to LjSK1 provided their structure-activity relationship and showed that hederacoside C can be the starting point for such endeavors.


  • Organizational Affiliation

    Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis 41500 Larissa, Greece.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
non-specific serine/threonine protein kinase466Lotus japonicusMutation(s): 0 
EC: 2.7.11.1
UniProt
Find proteins for Q53VM1 (Lotus japonicus)
Explore Q53VM1 
Go to UniProtKB:  Q53VM1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ53VM1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
PTR
Query on PTR
A
L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.250 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.318α = 90
b = 69.323β = 90
c = 99.641γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-21
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Database references