2VUR | pdb_00002vur

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.241 (Depositor), 0.197 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1016/j.chembiol.2008.06.010
  • Primary Citation Related Structures: 
    2VUR

  • 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-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.

Macromolecule Content 

  • Total Structure Weight: 134.01 kDa 
  • Atom Count: 9,809 
  • Modeled Residue Count: 1,168 
  • Deposited Residue Count: 1,188 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
O-GLCNACASE NAGJ
A, B
594Clostridium perfringensMutation(s): 0 
EC: 3.2.1.35 (PDB Primary Data), 3.2.1.169 (UniProt)
UniProt
Find proteins for Q0TR53 (Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A))
Explore Q0TR53 
Go to UniProtKB:  Q0TR53
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0TR53
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.241 (Depositor), 0.197 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.191 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.47α = 90
b = 149.731β = 90
c = 152.121γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-02-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Structure summary