Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content

• Total Structure Weight: 49.84 kDa 
• Atom Count: 3761 
• Modelled Residue Count: 407 
• Deposited Residue Count: 432 
• Unique protein chains: 2

5XVE

Crystal structure of human USP2 C276S mutant in complex with ubiquitin

• PDB DOI: 10.2210/pdb5XVE/pdb

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


• Deposited: 2017-06-27 Released: 2018-02-28 
• Deposition Author(s): Chou, C.Y., Tang, H.C.
• Funding Organization(s): Ministry of Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free: 0.164 
• R-Value Work: 0.147 
• R-Value Observed: 0.148 

Literature

6-Thioguanine is a noncompetitive and slow binding inhibitor of human deubiquitinating protease USP2

Chuang, S.J., Cheng, S.C., Tang, H.C., Sun, C.Y., Chou, C.Y.

(2018) Sci Rep 8: 3102-3102

• PubMed: 29449607 
• DOI: 10.1038/s41598-018-21476-w
• Primary Citation of Related Structures:  
  5XU8, 5XVE


• PubMed Abstract: 
  

Ubiquitin-specific protease 2 (USP2) belongs to the family of deubiquitinases that can rescue protein targets from proteasomal degradation by reversing their ubiquitination. In various cancers, including prostate cancer and ovarian carcinoma, upregulation of USP2 leads to an increase in the levels of deubiquitinated substrates such as fatty acid synthase, MDM2, cyclin D1 and Aurora-A. USP2 thus plays a critical role in tumor cells' survival and therefore represents a therapeutic target. Here a leukemia drug, 6-thioguanine, was found to be a potent inhibitor of USP2. Enzyme-kinetic and X-ray crystallographic data suggest that 6-thioguanine displays a noncompetitive and slow-binding inhibitory mechanism against USP2. Our study provides a clear rationale for the clinical evaluation of 6-thioguanine for USP2-upregulated cancers.

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Organizational Affiliation: 

Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, 112, Taiwan. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin carboxyl-terminal hydrolase 2	A	356	Homo sapiens	Mutation(s): 0  Gene Names: USP2, UBP41 EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for O75604 (Homo sapiens) Explore O75604  Go to UniProtKB:  O75604
PHAROS:  O75604 GTEx:  ENSG00000036672

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-40S ribosomal protein S27a	B	76	Bos taurus	Mutation(s): 0  Gene Names: RPS27A, UBA80, UBCEP1
UniProt
Find proteins for P62992 (Bos taurus) Explore P62992  Go to UniProtKB:  P62992

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.24 Å
• R-Value Free: 0.164 
• R-Value Work: 0.147 
• R-Value Observed: 0.148 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.473	α = 90
b = 54.011	β = 107.79
c = 74.753	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data processing
PHASER	model building
HKL-2000	data reduction
PHASER	phasing
HKL-2000	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-06-27 
• Released Date: 2018-02-28 
Deposition Author(s): Chou, C.Y., Tang, H.C.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology	Taiwan	105-2320-B-010-012
Ministry of Science and Technology	Taiwan	104-2320-B-010-034

Revision History  

• Version 1.0: 2018-02-28
  Type: Initial release