3C58

Crystal structure of a complex between the wild-type lactococcus lactis Fpg (MutM) and a N7-Benzyl-Fapy-dG containing DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Bacterial base excision repair enzyme Fpg recognizes bulky N7-substituted-FapydG lesion via unproductive binding mode

Coste, F.Ober, M.Le Bihan, Y.V.Izquierdo, M.A.Hervouet, N.Mueller, H.Carell, T.Castaing, B.

(2008) Chem.Biol. 15: 706-717

  • DOI: 10.1016/j.chembiol.2008.05.014

  • PubMed Abstract: 
  • Fpg is a bacterial base excision repair enzyme that removes oxidized purines from DNA. This work shows that Fpg and its eukaryote homolog Ogg1 recognize with high affinity FapydG and bulky N7-benzyl-FapydG (Bz-FapydG). The comparative crystal structu ...

    Fpg is a bacterial base excision repair enzyme that removes oxidized purines from DNA. This work shows that Fpg and its eukaryote homolog Ogg1 recognize with high affinity FapydG and bulky N7-benzyl-FapydG (Bz-FapydG). The comparative crystal structure analysis of stable complexes between Fpg and carbocyclic cFapydG or Bz-cFapydG nucleoside-containing DNA provides the molecular basis of the ability of Fpg to bind both lesions with the same affinity and to differently process them. To accommodate the steric hindrance of the benzyl group, Fpg selects the adequate rotamer of the extrahelical Bz-cFapydG formamido group, forcing the bulky group to go outside the binding pocket. Contrary to the binding mode of cFapydG, the particular recognition of Bz-cFapydG leads the BER enzymes to unproductive complexes which would hide the lesion and slow down its repair by the NER machinery.


    Organizational Affiliation

    Centre de Biophysique Moléculaire, UPR4301, CNRS, rue Charles Sadron, 45071 Orléans cedex 02, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA glycosylase
A
271Lactococcus lactis subsp. cremorisGene Names: mutM (fpg)
EC: 3.2.2.23, 4.2.99.18
Find proteins for P42371 (Lactococcus lactis subsp. cremoris)
Go to UniProtKB:  P42371
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*DGP*DCP*DGP*DAP*DGP*DAP*DAP*DAP*DCP*DAP*DAP*DAP*DGP*DA)-3')C14N/A
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*DCP*DTP*DCP*DTP*DTP*DTP*(SOS)P*DTP*DTP*DTP*DCP*DTP*DCP*DG)-3')B14N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-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: 1.9 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.172 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 91.356α = 90.00
b = 91.356β = 90.00
c = 140.943γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
AMoREphasing
MOSFLMdata reduction
DNAdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance