spacer
spacer

PDBsum entry 1kfv

Go to PDB code: 
Top Page protein dna_rna ligands metals Protein-protein interface(s) links
Hydrolase/DNA PDB id
1kfv
Jmol
Contents
Protein chains
264 a.a. *
DNA/RNA
Ligands
GOL ×2
Metals
_ZN ×2
Waters ×54
* Residue conservation analysis

References listed in PDB file
Key reference
Title Crystal structure of the lactococcus lactis formamidopyrimidine-Dna glycosylase bound to an abasic site analogue-Containing DNA.
Authors L.Serre, K.Pereira de jésus, S.Boiteux, C.Zelwer, B.Castaing.
Ref. Embo J, 2002, 21, 2854-2865. [DOI no: 10.1093/emboj/cdf304]
PubMed id 12065399
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.
Figure 6.
Figure 6 Stereo view of Fpg contacts around the Pr abasic site analogue. Hydrogen bonds are indicated by dashed lines. DNA atoms are represented by orange ball-and-sticks, and mutagenesis targeted amino acids are underlined (see text for details). The figures were generated by Molscript (Kraulis et al., 1991) and Raster3-D (Merritt and Murphy, 1994).
Figure 8.
Figure 8 Recognition of the C20 opposite the Pr site by R109. Stereo view showing the intercalation of the Fpg triad by the minor groove and the pseudo-Watson−Crick interactions between R109 and C20. Hydrogen bonds are indicated by dashed lines. The atomic coordinates of the triad (M70/R99/F101) from the free TtFpg have been superposed and are represented by green ball-and-sticks. The figure was generated by Molscript (Kraulis et al., 1991) and Raster3-D (Merritt and Murphy, 1994).
The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2002, 21, 2854-2865) copyright 2002.
PROCHECK
Go to PROCHECK summary
 Headers

 

spacer

spacer