5XU8

Crystal structure of human USP2 in complex with ubiquitin and 6-thioguanine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

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:  

  • 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, upregul ...

    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 Nephrology, Chang-Gung Memorial Hospital, Keelung, 204, Taiwan.,Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, 112, Taiwan.,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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin carboxyl-terminal hydrolase 2
A
356Homo 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
Ubiquitin-40S ribosomal protein S27a
B
76Bos taurusMutation(s): 0 
Gene Names: RPS27A (UBA80, UBCEP1)
Find proteins for P62992 (Bos taurus)
Go to Gene View: RPS27A
Go to UniProtKB:  P62992
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DX4
Query on DX4

Download SDF File 
Download CCD File 
A
2-amino-1,9-dihydro-6H-purine-6-thione
C5 H5 N5 S
WYWHKKSPHMUBEB-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.81 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.179 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 102.953α = 90.00
b = 54.650β = 107.54
c = 72.687γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
REFMACrefinement
HKL-2000data reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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