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PDBsum entry 1pm5

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Hydrolase/DNA PDB id
1pm5
Jmol
Contents
Protein chain
271 a.a. *
DNA/RNA
Ligands
GOL ×3
Metals
_ZN
Waters ×306
* Residue conservation analysis

References listed in PDB file
Key reference
Title 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.
Authors K.Pereira de jésus, L.Serre, C.Zelwer, B.Castaing.
Ref. Nucleic Acids Res, 2005, 33, 5936-5944.
PubMed id 16243784
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 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.
Secondary reference #1
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
Full text Abstract
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 reproduced from the cited reference which is an Open Access publication published by Macmillan Publishers Ltd
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