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 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1093/emboj/cdf304

  • 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 damag ...

    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

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Formamido-pyrimidine DNA glycosylase
A, B
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
5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*C)-3'D,G13N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*AP*G)-3'E,H13N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
PDI
Query on PDI
D, G
NON-POLYMERC3 H9 O5 P

--

MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
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 = 69.880α = 90.00
b = 62.030β = 104.70
c = 80.970γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
CCP4data scaling
CNSrefinement
MOLREPphasing
DENZOdata reduction
SnBphasing
SHAKE-N-BAKEphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance