2VUR

Chemical dissection of the link between Streptozotocin, O-GlcNAc and pancreatic cell death


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Chemical Dissection of the Link between Streptozotocin, O-Glcnac, and Pancreatic Cell Death.

Pathak, S.Dorfmueller, H.C.Borodkin, V.S.Van Aalten, D.M.F.

(2008) Chem.Biol. 15: 799

  • DOI: 10.1016/j.chembiol.2008.06.010

  • PubMed Abstract: 
  • Streptozotocin is a natural product that selectively kills insulin-secreting beta cells, and is widely used to generate mouse models of diabetes or treat pancreatic tumors. Several studies suggest that streptozotocin toxicity stems from its N-nitroso ...

    Streptozotocin is a natural product that selectively kills insulin-secreting beta cells, and is widely used to generate mouse models of diabetes or treat pancreatic tumors. Several studies suggest that streptozotocin toxicity stems from its N-nitrosourea moiety releasing nitric oxide and possessing DNA alkylating activity. However, it has also been proposed that streptozotocin induces apoptosis by inhibiting O-GlcNAcase, an enzyme that, together with O-GlcNAc transferase, is important for dynamic intracellular protein O-glycosylation. We have used galacto-streptozotocin to chemically dissect the link between O-GlcNAcase inhibition and apoptosis. Using X-ray crystallography, enzymology, and cell biological studies on an insulinoma cell line, we show that, whereas streptozotocin competitively inhibits O-GlcNAcase and induces apoptosis, its galacto-configured derivative no longer inhibits O-GlcNAcase, yet still induces apoptosis. This supports a general chemical poison mode of action for streptozotocin, suggesting the need for using more specific inhibitors to study protein O-GlcNAcylation.


    Organizational Affiliation

    Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee, Scotland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
O-GLCNACASE NAGJ
A, B
594Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A)Mutation(s): 0 
Gene Names: nagJ
EC: 3.2.1.169
Find proteins for Q0TR53 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A))
Go to UniProtKB:  Q0TR53
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
YX1
Query on YX1

Download SDF File 
Download CCD File 
A, B
2-deoxy-2-{[(2-hydroxy-1-methylhydrazino)carbonyl]amino}-beta-D-glucopyranose
C8 H17 N3 O7
LUNQAAUVSFIVKD-NYMZXIIRSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
YX1IC50: 30000 nM BINDINGMOAD
YX1IC50: 30000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.195 
  • Space Group: I 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 130.470α = 90.00
b = 149.731β = 90.00
c = 152.121γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-02-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance