2XZU

CRYSTAL STRUCTURE OF A COMPLEX BETWEEN THE WILD-TYPE LACTOCOCCUS LACTIS FPG (MUTM) AND AN OXIDIZED PYRIMIDINE CONTAINING DNA AT 310K


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 

Starting Model: experimental
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This is version 1.2 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: https://doi.org/10.1093/nar/gkr215
  • Primary Citation of Related Structures:  
    2XZF, 2XZU

  • 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 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

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE271Lactococcus cremorisMutation(s): 0 
EC: 3.2.2.23 (PDB Primary Data), 4.2.99.18 (PDB Primary Data)
UniProt
Find proteins for P42371 (Lactococcus lactis subsp. cremoris)
Explore P42371 
Go to UniProtKB:  P42371
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP42371
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*CP*TP*CP*TP*TP*TP*VETP*TP*TP*TP*CP*TP*CP*G)-3'14synthetic construct
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*G*A)-3'14synthetic construct
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.157 
  • R-Value Observed: 0.159 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.739α = 90
b = 91.739β = 90
c = 143.236γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-10-05
    Type: Initial release
  • Version 1.1: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.2: 2024-10-16
    Changes: Structure summary