4WPH

Crystal structure of USP7 ubiquitin-like domains in compact conformation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of USP7 Ubiquitin-like Domains with an ICP0 Peptide Reveals a Novel Mechanism Used by Viral and Cellular Proteins to Target USP7.

Pfoh, R.Lacdao, I.K.Georges, A.A.Capar, A.Zheng, H.Frappier, L.Saridakis, V.

(2015) PLoS Pathog 11: e1004950-e1004950

  • DOI: 10.1371/journal.ppat.1004950
  • Primary Citation of Related Structures:  
    4WPH, 4WPI

  • PubMed Abstract: 
  • Herpes simplex virus-1 immediate-early protein ICP0 activates viral genes during early stages of infection, affects cellular levels of multiple host proteins and is crucial for effective lytic infection. Being a RING-type E3 ligase prone to auto-ubiq ...

    Herpes simplex virus-1 immediate-early protein ICP0 activates viral genes during early stages of infection, affects cellular levels of multiple host proteins and is crucial for effective lytic infection. Being a RING-type E3 ligase prone to auto-ubiquitination, ICP0 relies on human deubiquitinating enzyme USP7 for protection against 26S proteasomal mediated degradation. USP7 is involved in apoptosis, epigenetics, cell proliferation and is targeted by several herpesviruses. Several USP7 partners, including ICP0, GMPS, and UHRF1, interact through its C-terminal domain (CTD), which contains five ubiquitin-like (Ubl) structures. Despite the fact that USP7 has emerged as a drug target for cancer therapy, structural details of USP7 regulation and the molecular mechanism of interaction at its CTD have remained elusive. Here, we mapped the binding site between an ICP0 peptide and USP7 and determined the crystal structure of the first three Ubl domains bound to the ICP0 peptide, which showed that ICP0 binds to a loop on Ubl2. Sequences similar to the USP7-binding site in ICP0 were identified in GMPS and UHRF1 and shown to bind USP7-CTD through Ubl2. In addition, co-immunoprecipitation assays in human cells comparing binding to USP7 with and without a Ubl2 mutation, confirmed the importance of the Ubl2 binding pocket for binding ICP0, GMPS and UHRF1. Therefore we have identified a novel mechanism of USP7 recognition that is used by both viral and cellular proteins. Our structural information was used to generate a model of near full-length USP7, showing the relative position of the ICP0/GMPS/UHRF1 binding pocket and the structural basis by which it could regulate enzymatic activity.


    Organizational Affiliation

    Department of Biology, York University, Toronto, Ontario, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 7AB375Homo sapiensMutation(s): 0 
Gene Names: USP7HAUSP
EC: 3.4.19.12
Find proteins for Q93009 (Homo sapiens)
Explore Q93009 
Go to UniProtKB:  Q93009
NIH Common Fund Data Resources
PHAROS  Q93009
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ICP0CD11Human alphaherpesvirus 1 strain 17Mutation(s): 0 
Gene Names: ICP0IE110
EC: 2.3.2.27
Find proteins for P08393 (Human herpesvirus 1 (strain 17))
Explore P08393 
Go to UniProtKB:  P08393
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.336α = 90
b = 92.336β = 90
c = 190.283γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)Canada106583

Revision History 

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence, Derived calculations, Other, Source and taxonomy
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence