4PCZ

Crystal structure of a complex between R247G LlFPG mutant and a THF containing DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Zinc finger oxidation of Fpg/Nei DNA glycosylases by 2-thioxanthine: biochemical and X-ray structural characterization.

Biela, A.Coste, F.Culard, F.Guerin, M.Goffinont, S.Gasteiger, K.Ciesla, J.Winczura, A.Kazimierczuk, Z.Gasparutto, D.Carell, T.Tudek, B.Castaing, B.

(2014) Nucleic Acids Res 42: 10748-10761

  • DOI: 10.1093/nar/gku613
  • Primary Citation of Related Structures:  
    4PDG, 4PCZ, 4PD2, 4PDI

  • PubMed Abstract: 
  • DNA glycosylases from the Fpg/Nei structural superfamily are base excision repair enzymes involved in the removal of a wide variety of mutagen and potentially lethal oxidized purines and pyrimidines. Although involved in genome stability, the recent discovery of synthetic lethal relationships between DNA glycosylases and other pathways highlights the potential of DNA glycosylase inhibitors for future medicinal chemistry development in cancer therapy ...

    DNA glycosylases from the Fpg/Nei structural superfamily are base excision repair enzymes involved in the removal of a wide variety of mutagen and potentially lethal oxidized purines and pyrimidines. Although involved in genome stability, the recent discovery of synthetic lethal relationships between DNA glycosylases and other pathways highlights the potential of DNA glycosylase inhibitors for future medicinal chemistry development in cancer therapy. By combining biochemical and structural approaches, the physical target of 2-thioxanthine (2TX), an uncompetitive inhibitor of Fpg, was identified. 2TX interacts with the zinc finger (ZnF) DNA binding domain of the enzyme. This explains why the zincless hNEIL1 enzyme is resistant to 2TX. Crystal structures of the enzyme bound to DNA in the presence of 2TX demonstrate that the inhibitor chemically reacts with cysteine thiolates of ZnF and induces the loss of zinc. The molecular mechanism by which 2TX inhibits Fpg may be generalized to all prokaryote and eukaryote ZnF-containing Fpg/Nei-DNA glycosylases. Cell experiments show that 2TX can operate in cellulo on the human Fpg/Nei DNA glycosylases. The atomic elucidation of the determinants for the interaction of 2TX to Fpg provides the foundation for the future design and synthesis of new inhibitors with high efficiency and selectivity.


    Organizational Affiliation

    Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45100 Orléans cedex02, France castaing@cnrs-orleans.fr.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Formamidopyrimidine-DNA glycosylaseA271Lactococcus cremorisMutation(s): 1 
Gene Names: mutMfpg
EC: 3.2.2.23 (PDB Primary Data), 4.2.99.18 (UniProt)
UniProt
Find proteins for P42371 (Lactococcus lactis subsp. cremoris)
Explore P42371 
Go to UniProtKB:  P42371
Protein Feature View
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  • Reference Sequence
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  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)-3')B14synthetic construct
    Protein Feature View
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    • Reference Sequence
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    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3')C14synthetic construct
      Protein Feature View
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      • Reference Sequence
      Small Molecules
      Ligands 2 Unique
      IDChainsName / Formula / InChI Key2D Diagram3D Interactions
      GOL
      Query on GOL

      Download Ideal Coordinates CCD File 
      E [auth A]GLYCEROL
      C3 H8 O3
      PEDCQBHIVMGVHV-UHFFFAOYSA-N
       Ligand Interaction
      ZN
      Query on ZN

      Download Ideal Coordinates CCD File 
      D [auth A]ZINC ION
      Zn
      PTFCDOFLOPIGGS-UHFFFAOYSA-N
       Ligand Interaction
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.70 Å
      • R-Value Free: 0.181 
      • R-Value Work: 0.157 
      • R-Value Observed: 0.158 
      • Space Group: P 41 21 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 91.723α = 90
      b = 91.723β = 90
      c = 142.32γ = 90
      Software Package:
      Software NamePurpose
      PHENIXrefinement

      Structure Validation

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      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2015-04-01
        Type: Initial release