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PDBsum entry 1pjj

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Hydrolase/DNA PDB id
1pjj
Jmol
Contents
Protein chain
271 a.a. *
DNA/RNA
Ligands
GOL ×3
Metals
_ZN
Waters ×278
* 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 Crystallization and preliminary X-Ray crystallographic studies of a complex between the lactococcus lactis fpg DNA-Repair enzyme and an abasic site containing DNA.
Authors K.Pereira de jésus, L.Serre, N.Hervouet, V.Bouckson-Castaing, C.Zelwer, B.Castaing.
Ref. Acta Crystallogr D Biol Crystallogr, 2002, 58, 679-682. [DOI no: 10.1107/S0907444902001397]
PubMed id 11914495
Full text Abstract
Figure 2.
Figure 2 Oligonucleotides used for the crystallization assays. AP-site analogue containing strands (up) were annealed with their complementary strands (low) to generate 13-mer and 15-mer DNA duplexes (up/low) with blunt ends or one complementary 3' or 5' overhanging base ends. In all DNA duplexes, the 1,3-propanediol (X) or tetrahydrofuran (Y) site analogue was opposite the bold cytosine. (1) and (2) indicate the 13-mer sequences used in this study.
The above figure is reproduced from the cited reference with permission from the IUCr
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