2XZF

CRYSTAL STRUCTURE OF A COMPLEX BETWEEN THE WILD-TYPE LACTOCOCCUS LACTIS FPG (MUTM) AND AN OXIDIZED PYRIMIDINE CONTAINING DNA AT 293K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.799 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

5-Hydroxy-5-Methylhydantoin DNA Lesion, a Molecular Trap for DNA Glycosylases

Le Bihan, Y.V.Izquierdo, M.A.Coste, F.Aller, P.Culard, F.Gehrke, T.H.Essalhi, K.Carrel, T.Castaing, B.

(2011) Nucleic Acids Res. 39: 6277

  • DOI: 10.1093/nar/gkr215
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • DNA base-damage recognition in the base excision repair (BER) is a process operating on a wide variety of alkylated, oxidized and degraded bases. DNA glycosylases are the key enzymes which initiate the BER pathway by recognizing and excising the base ...

    DNA base-damage recognition in the base excision repair (BER) is a process operating on a wide variety of alkylated, oxidized and degraded bases. DNA glycosylases are the key enzymes which initiate the BER pathway by recognizing and excising the base damages guiding the damaged DNA through repair synthesis. We report here biochemical and structural evidence for the irreversible entrapment of DNA glycosylases by 5-hydroxy-5-methylhydantoin, an oxidized thymine lesion. The first crystal structure of a suicide complex between DNA glycosylase and unrepaired DNA has been solved. In this structure, the formamidopyrimidine-(Fapy) DNA glycosylase from Lactococcus lactis (LlFpg/LlMutM) is covalently bound to the hydantoin carbanucleoside-containing DNA. Coupling a structural approach by solving also the crystal structure of the non-covalent complex with site directed mutagenesis, this atypical suicide reaction mechanism was elucidated. It results from the nucleophilic attack of the catalytic N-terminal proline of LlFpg on the C5-carbon of the base moiety of the hydantoin lesion. The biological significance of this finding is discussed.


    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: 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
5'-D(*CP*TP*CP*TP*TP*TP*VETP*TP*TP*TP*CP*TP*CP*GP)-3'B14synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*AP*GP*CP)-3'C14synthetic construct
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

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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
VET
Query on VET
B
DNA LINKINGC10 H17 N2 O8 P

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.799 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.160 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 91.569α = 90.00
b = 91.569β = 90.00
c = 142.777γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PHENIXphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-10-05
    Type: Initial release