5O71

Crystal structure of human USP25


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.283 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A quaternary tetramer assembly inhibits the deubiquitinating activity of USP25.

Liu, B.Sureda-Gomez, M.Zhen, Y.Amador, V.Reverter, D.

(2018) Nat Commun 9: 4973-4973

  • DOI: 10.1038/s41467-018-07510-5

  • PubMed Abstract: 
  • USP25 deubiquitinating enzyme is a key member of the ubiquitin system, which acts as a positive regulator of the Wnt/β-catenin signaling by promoting the deubiquitination and stabilization of tankyrases. USP25 is characterized by the presence of a lo ...

    USP25 deubiquitinating enzyme is a key member of the ubiquitin system, which acts as a positive regulator of the Wnt/β-catenin signaling by promoting the deubiquitination and stabilization of tankyrases. USP25 is characterized by the presence of a long insertion in the middle of the conserved catalytic domain. The crystal structure of USP25 displays an unexpected homotetrameric quaternary assembly that is directly involved in the inhibition of its enzymatic activity. The tetramer is assembled by the association of two dimers and includes contacts between the coiled-coil insertion domain and the ubiquitin-binding pocket at the catalytic domain, revealing a distinctive autoinhibitory mechanism. Biochemical and kinetic assays with dimer, tetramer and truncation constructs of USP25 support this mechanism, displaying higher catalytic activity in the dimer assembly. Moreover, the high stabilization of tankyrases in cultured cells by ectopic expression of a constitutive dimer of USP25 supports a biological relevance of this tetramerization/inhibition mechanism.


    Organizational Affiliation

    Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.,Institut de Investigacions Biomèdiques Agustí Pi i Sunyer (IDIBABS), Barcelona, 08036, Spain.,Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain. david.reverter@uab.cat.,Dept. de Bioquímica i Biologia Molecular, Serra Hunter Fellow, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain. david.reverter@uab.cat.,Dept. de Bioquímica i Biologia Molecular, Serra Hunter Fellow, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin carboxyl-terminal hydrolase 25
A
716Homo sapiensMutation(s): 0 
Gene Names: USP25 (USP21)
EC: 3.4.19.12
Find proteins for Q9UHP3 (Homo sapiens)
Go to Gene View: USP25
Go to UniProtKB:  Q9UHP3
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.283 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.202 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 140.806α = 90.00
b = 140.806β = 90.00
c = 190.156γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PHENIXphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2017-06-07 
  • Released Date: 2018-06-20 
  • Deposition Author(s): Reverter, D., Liu, B.

Funding OrganizationLocationGrant Number
Spanish Ministry of Economy and CompetitivenessSpainBFU2015-66417

Revision History 

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2019-04-17
    Type: Data collection, Database references