2HD5

USP2 in complex with ubiquitin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Basis of Ubiquitin Recognition by the Deubiquitinating Protease USP2.

Renatus, M.Parrado, S.G.D'Arcy, A.Eidhoff, U.Gerhartz, B.Hassiepen, U.Pierrat, B.Riedl, R.Vinzenz, D.Worpenberg, S.Kroemer, M.

(2006) Structure 14: 1293-1302

  • DOI: 10.1016/j.str.2006.06.012

  • PubMed Abstract: 
  • Deubiquitinating proteases reverse protein ubiquitination and rescue their target proteins from destruction by the proteasome. USP2, a cysteine protease and a member of the ubiquitin specific protease family, is overexpressed in prostate cancer and s ...

    Deubiquitinating proteases reverse protein ubiquitination and rescue their target proteins from destruction by the proteasome. USP2, a cysteine protease and a member of the ubiquitin specific protease family, is overexpressed in prostate cancer and stabilizes fatty acid synthase, which has been associated with the malignancy of some aggressive prostate cancers. Here, we report the structure of the human USP2 catalytic domain in complex with ubiquitin. Ubiquitin uses two major sites for the interaction with the protease. Both sites are required simultaneously, as shown by USP2 inhibition assays with peptides and ubiquitin mutants. In addition, a layer of ordered water molecules mediates key interactions between ubiquitin and USP2. As several of those molecules are found at identical positions in the previously solved USP7/ubiquitin-aldehyde complex structure, we suggest a general mechanism of water-mediated ubiquitin recognition by USPs.


    Organizational Affiliation

    Protease Platform, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland. martin.renatus@novartis.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin carboxyl-terminal hydrolase 2
A
359Homo sapiensMutation(s): 0 
Gene Names: USP2 (UBP41)
EC: 3.4.19.12
Find proteins for O75604 (Homo sapiens)
Go to Gene View: USP2
Go to UniProtKB:  O75604
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin
B
76Bos taurusMutation(s): 0 
Gene Names: UBC
Find proteins for P0CH28 (Bos taurus)
Go to Gene View: UBC
Go to UniProtKB:  P0CH28
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.177 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 106.903α = 90.00
b = 45.534β = 110.01
c = 76.360γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PHASERphasing
CrystalCleardata reduction
CNSrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CNXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-08-15
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description