8WWR

Crystal structure of apo human dishevelled 2 (Dvl2) PDZ domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Dishevelled2 activates WGEF via its interaction with a unique internal peptide motif of the GEF.

Omble, A.Mahajan, S.Bhoite, A.Kulkarni, K.

(2024) Commun Biol 7: 543-543

  • DOI: https://doi.org/10.1038/s42003-024-06194-6
  • Primary Citation of Related Structures:  
    8WWR, 8YR7

  • PubMed Abstract: 

    The Wnt-planar cell polarity (Wnt-PCP) pathway is crucial in establishing cell polarity during development and tissue homoeostasis. This pathway is found to be dysregulated in many pathological conditions, including cancer and autoimmune disorders. The central event in Wnt-PCP pathway is the activation of Weak-similarity guanine nucleotide exchange factor (WGEF) by the adapter protein Dishevelled (Dvl). The PDZ domain of Dishevelled2 (Dvl2 PDZ ) binds and activates WGEF by releasing it from its autoinhibitory state. However, the actual Dvl2 PDZ binding site of WGEF and the consequent activation mechanism of the GEF have remained elusive. Using biochemical and molecular dynamics studies, we show that a unique "internal-PDZ binding motif" (IPM) of WGEF mediates the WGEF-Dvl2 PDZ interaction to activate the GEF. The residues at P 2 , P 0 , P -2 and P -3 positions of IPM play an important role in stabilizing the WGEF pep -Dvl2 PDZ interaction. Furthermore, MD simulations of modelled Dvl2 PDZ -WGEF IPM peptide complexes suggest that WGEF-Dvl2 PDZ interaction may differ from the reported Dvl2 PDZ -IPM interactions. Additionally, the apo structure of human Dvl2 PDZ shows conformational dynamics different from its IPM peptide bound state, suggesting an induced fit mechanism for the Dvl2 PDZ -peptide interaction. The current study provides a model for Dvl2 induced activation of WGEF.


  • Organizational Affiliation

    Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune, 411008, India.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Segment polarity protein dishevelled homolog DVL-295Homo sapiensMutation(s): 0 
Gene Names: DVL2
UniProt & NIH Common Fund Data Resources
Find proteins for O14641 (Homo sapiens)
Explore O14641 
Go to UniProtKB:  O14641
GTEx:  ENSG00000004975 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO14641
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.228 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.978α = 90
b = 45.978β = 90
c = 78.422γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Council of Scientific & Industrial Research (CSIR)India--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-29
    Type: Initial release