5XVE

Crystal structure of human USP2 C276S mutant in complex with ubiquitin

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 

wwPDB Validation   3D Report Full Report



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

  • 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, upregulatio ...

    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.

    Organizational Affiliation: 

    Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, 112, Taiwan. cychou@ym.edu.tw.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 2 A356Homo sapiensMutation(s): 0 
Gene Names: USP2, UBP41
EC: 3.4.19.12
Find proteins for O75604 (Homo sapiens)
Explore O75604 
Go to UniProtKB:  O75604
NIH Common Fund Data Resources
PHAROS:  O75604
GTEx:  ENSG00000036672
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-40S ribosomal protein S27a B76Bos taurusMutation(s): 0 
Gene Names: RPS27A, UBA80, UBCEP1
Find proteins for P62992 (Bos taurus)
Explore P62992 
Go to UniProtKB:  P62992
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
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 = 102.473α = 90
b = 54.011β = 107.79
c = 74.753γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data processing
PHASERmodel building
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling

Structure Validation

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View more in-depth experimental data

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.
Funding OrganizationLocationGrant Number
Ministry of Science and TechnologyTaiwan105-2320-B-010-012
Ministry of Science and TechnologyTaiwan104-2320-B-010-034

Revision History 

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