5SXP

STRUCTURAL BASIS FOR THE INTERACTION BETWEEN ITCH PRR AND BETA-PIX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Molecular basis of interactions between SH3 domain-containing proteins and the proline-rich region of the ubiquitin ligase Itch.

Desrochers, G.Cappadocia, L.Lussier-Price, M.Ton, A.T.Ayoubi, R.Serohijos, A.Omichinski, J.G.Angers, A.

(2017) J Biol Chem 292: 6325-6338

  • DOI: 10.1074/jbc.M116.754440
  • Primary Citation of Related Structures:  
    5SXP

  • PubMed Abstract: 
  • The ligase Itch plays major roles in signaling pathways by inducing ubiquitylation-dependent degradation of several substrates. Substrate recognition and binding are critical for the regulation of this reaction. Like closely related ligases, Itch can interact with proteins containing a PP X Y motif via its WW domains ...

    The ligase Itch plays major roles in signaling pathways by inducing ubiquitylation-dependent degradation of several substrates. Substrate recognition and binding are critical for the regulation of this reaction. Like closely related ligases, Itch can interact with proteins containing a PP X Y motif via its WW domains. In addition to these WW domains, Itch possesses a proline-rich region (PRR) that has been shown to interact with several Src homology 3 (SH3) domain-containing proteins. We have previously established that despite the apparent surface uniformity and conserved fold of SH3 domains, they display different binding mechanisms and affinities for their interaction with the PRR of Itch. Here, we attempt to determine the molecular bases underlying the wide range of binding properties of the Itch PRR. Using pulldown assays combined with mass spectrometry analysis, we show that the Itch PRR preferentially forms complexes with endophilins, amphyphisins, and pacsins but can also target a variety of other SH3 domain-containing proteins. In addition, we map the binding sites of these proteins using a combination of PRR sub-sequences and mutants. We find that different SH3 domains target distinct proline-rich sequences overlapping significantly. We also structurally analyze these protein complexes using crystallography and molecular modeling. These structures depict the position of Itch PRR engaged in a 1:2 protein complex with β-PIX and a 1:1 complex with the other SH3 domain-containing proteins. Taken together, these results reveal the binding preferences of the Itch PRR toward its most common SH3 domain-containing partners and demonstrate that the PRR region is sufficient for binding.


    Organizational Affiliation

    From the Departments of Biological Sciences and annie.angers@umontreal.ca.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Rho guanine nucleotide exchange factor 7A, B, C, D62Homo sapiensMutation(s): 0 
Gene Names: ARHGEF7COOL1KIAA0142P85SPRPAK3BPPIXBNbla10314
UniProt & NIH Common Fund Data Resources
Find proteins for Q14155 (Homo sapiens)
Explore Q14155 
Go to UniProtKB:  Q14155
PHAROS:  Q14155
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14155
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase Itchy homologE [auth F],
F [auth G]
27Homo sapiensMutation(s): 0 
Gene Names: ITCH
EC: 6.3.2 (PDB Primary Data), 2.3.2.26 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96J02 (Homo sapiens)
Explore Q96J02 
Go to UniProtKB:  Q96J02
PHAROS:  Q96J02
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96J02
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.161 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.140 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 28.845α = 90.37
b = 43.451β = 101.01
c = 61.482γ = 105.25
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)Canada312158

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-01
    Type: Initial release
  • Version 1.1: 2017-03-15
    Changes: Data collection, Database references
  • Version 1.2: 2017-04-26
    Changes: Database references
  • Version 1.3: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.4: 2020-01-08
    Changes: Author supporting evidence