Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 50.07 kDa 
• Atom Count: 3287 
• Residue Count: 391 
• Unique protein chains: 2

2HD5

USP2 in complex with ubiquitin

• DOI: 10.2210/pdb2HD5/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens, Bos taurus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-06-20 Released: 2006-08-15 
• Deposition Author(s): Renatus, M., Kroemer, M.

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Experimental Data Snapshot

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

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

• PubMed: 16905103 
• DOI: 10.1016/j.str.2006.06.012
• Primary Citation of Related Structures:  
  2HD5


• 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 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.

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Organizational Affiliation: 

Protease Platform, Novartis Institutes for BioMedical Research, 4002 Basel, Switzerland. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 2	A	359	Homo sapiens	Mutation(s): 0  Gene Names: USP2, UBP41 EC: 3.1.2.15 (PDB Primary Data), 3.4.19.12 (UniProt)
Find proteins for O75604 (Homo sapiens) Explore O75604  Go to UniProtKB:  O75604
NIH Common Fund Data Resources
PHAROS:  O75604 GTEx:  ENSG00000036672

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin	B	76	Bos taurus	Mutation(s): 0  Gene Names: UBC
Find proteins for P0CH28 (Bos taurus) Explore P0CH28  Go to UniProtKB:  P0CH28

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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 = 106.903	α = 90
b = 45.534	β = 110.01
c = 76.36	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-06-20 
• Released Date: 2006-08-15 
Deposition Author(s): Renatus, M., Kroemer, M.

Revision History 

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