1KFV

Crystal Structure of Lactococcus lactis Formamido-pyrimidine DNA Glycosylase (alias Fpg or MutM) Non Covalently Bound to an AP Site Containing DNA.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.251 

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This is version 1.5 of the entry. See complete history. 


Literature

Crystal structure of the Lactococcus lactis formamidopyrimidine-DNA glycosylase bound to an abasic site analogue-containing DNA.

Serre, L., Pereira de Jesus, K., Boiteux, S., Zelwer, C., Castaing, B.

(2002) EMBO J 21: 2854-2865

  • DOI: https://doi.org/10.1093/emboj/cdf304
  • Primary Citation of Related Structures:  
    1KFV

  • PubMed Abstract: 

    The formamidopyrimidine-DNA glycosylase (Fpg, MutM) is a bifunctional base excision repair enzyme (DNA glycosylase/AP lyase) that removes a wide range of oxidized purines, such as 8-oxoguanine and imidazole ring-opened purines, from oxidatively damaged DNA. The structure of a non-covalent complex between the Lactoccocus lactis Fpg and a 1,3-propanediol (Pr) abasic site analogue-containing DNA has been solved. Through an asymmetric interaction along the damaged strand and the intercalation of the triad (M75/R109/F111), Fpg pushes out the Pr site from the DNA double helix, recognizing the cytosine opposite the lesion and inducing a 60 degrees bend of the DNA. The specific recognition of this cytosine provides some structural basis for understanding the divergence between Fpg and its structural homologue endo nuclease VIII towards their substrate specificities. In addition, the modelling of the 8-oxoguanine residue allows us to define an enzyme pocket that may accommodate the extrahelical oxidized base.

    • Organizational Affiliation: 

    Institut de Biologie Structurale, CNRS-CEA, 41 av. Jules Horowitz, 38027 Grenoble cedex 01, France.


Macromolecules

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Formamido-pyrimidine DNA glycosylaseE [auth A],
F [auth B]		271Lactococcus lactisMutation(s): 5 
Gene Names: MUTM or FPG
EC: 3.2.2.23
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: 1
MoleculeChains LengthOrganismImage
5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*C)-3'A [auth D],
C [auth G]		13N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
5'-D(*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*AP*G)-3'B [auth E],
D [auth H]		13N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.55 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.251 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.88α = 90
b = 62.03β = 104.7
c = 80.97γ = 90
Software Package:
Software NamePurpose
SnBphasing
SOLVEphasing
MOLREPphasing
CNSrefinement
DENZOdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-06-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations, Refinement description
  • Version 1.4: 2023-08-16
    Changes: Data collection, Refinement description
  • Version 1.5: 2023-11-15
    Changes: Data collection