1NNJ

Crystal structure Complex between the Lactococcus lactis Fpg and an abasic site containing DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA.

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

(2005) Nucleic Acids Res. 33: 5936-5944

  • DOI: 10.1093/nar/gki879
  • Primary Citation of Related Structures:  1PJI, 1PJJ, 1PM5

  • PubMed Abstract: 
  • Fpg is a DNA glycosylase that recognizes and excises the mutagenic 8-oxoguanine (8-oxoG) and the potentially lethal formamidopyrimidic residues (Fapy). Fpg is also associated with an AP lyase activity which successively cleaves the abasic (AP) site a ...

    Fpg is a DNA glycosylase that recognizes and excises the mutagenic 8-oxoguanine (8-oxoG) and the potentially lethal formamidopyrimidic residues (Fapy). Fpg is also associated with an AP lyase activity which successively cleaves the abasic (AP) site at the 3' and 5' sides by betadelta-elimination. Here, we present the high-resolution crystal structures of the wild-type and the P1G defective mutant of Fpg from Lactococcus lactis bound to 14mer DNA duplexes containing either a tetrahydrofuran (THF) or 1,3-propanediol (Pr) AP site analogues. Structures show that THF is less extrahelical than Pr and its backbone C5'-C4'-C3' diverges significantly from those of Pr, rAP, 8-oxodG and FapydG. Clearly, the heterocyclic oxygen of THF is pushed back by the carboxylate of the strictly conserved E2 residue. We can propose that the ring-opened form of the damaged deoxyribose is the structure active form of the sugar for Fpg catalysis process. Both structural and functional data suggest that the first step of catalysis mediated by Fpg involves the expulsion of the O4' leaving group facilitated by general acid catalysis (involving E2), rather than the immediate cleavage of the N-glycosic bond of the damaged nucleoside.


    Related Citations: 
    • Crystallization and primary X-ray crystallographic studies of a complex between the Lactococcus lactis Fpg DNA-repair enzyme and an abasic site containing DNA
      Pereira de Jesus, K.,Serre, L.,Hervouet, N.,Bouckson-Castaing, V.,Zelwer, C.,Castaing, B.
      (2002) Acta Crystallogr.,Sect.D 58: 679


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Formamidopyrimidine-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
5'-D(*CP*TP*CP*TP*TP*TP*(PDI)P*TP*TP*TP*CP*TP*CP*G)-3'D14N/A
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3'E14N/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, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
PDI
Query on PDI
D
NON-POLYMERC3 H9 O5 P

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DNAKd: 6 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.236 
  • R-Value Work: 0.215 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 92.150α = 90.00
b = 92.150β = 90.00
c = 142.530γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling
SCALAdata scaling
CNSrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-02-11
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance