4PDI

Crystal structure of a complex between an inhibited LlFpg and a N7-Benzyl-Fapy-dG containing DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.160 

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:  

  • 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 ...

    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 Institute of Biochemistry and Biophysics PAS, Pawinskiego 5A, 02-106 Warsaw, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Formamidopyrimidine-DNA glycosylase
A
271Lactococcus lactis subsp. cremorisMutation(s): 0 
Gene Names: mutM (fpg)
EC: 3.2.2.23
Find proteins for P42371 (Lactococcus lactis subsp. cremoris)
Go to UniProtKB:  P42371
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*TP*CP*TP*TP*TP*(SOS)P*TP*TP*TP*CP*TP*CP*G)-3')B14synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3')C14synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2ON
Query on 2ON

Download SDF File 
Download CCD File 
A
2-sulfanyl-1,9-dihydro-6H-purin-6-one
C5 H4 N4 O S
XNHFAGRBSMMFKL-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SOS
Query on SOS
B
DNA LINKINGC18 H24 N5 O7 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.160 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 91.535α = 90.00
b = 91.535β = 90.00
c = 140.974γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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