PROSITE documentation PDOC00956
Formamidopyrimidine-DNA glycosylase signature and profiles


Most damage to bases in DNA is repaired by the base excision repair pathway [1]. The repair is initiated by DNA glycosylases, enzymes that recognize specific lesion bases in DNA and remove them. Formamidopyrimidine-DNA glycosylase (EC (gene fpg) [2] is a bacterial DNA glycosylase that recognizes and removes damaged bases with a preference for oxidized purines, such as 7,8-dihydro-8-oxoguanine (8-oxoG). Excision of the oxidized guanine occurs via nucleophilic substitution at C1' by the N-terminal proline . The aminal intermediate thus formed rearranges to the Schiff base, which subsequently undergoes β- and delta-elimination, resulting in complete removal of the lesion nucleoside from DNA. FPG has thus also a nicking activity that cleaves both the 3'- and 5'-phosphodiester bonds at the apurinic/apyrimidinic (AP) site, leaving a gap in the DNA that has phosphate groups on both the 5'- and 3'-ends [3].

The protein contains three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger (see <PDB:1K82>) [4]. The N-terminal catalytic domain and the C-terminal zinc finger straddle the DNA with the long axis of the protein oriented roughly orthogonal to the helical axis of the DNA. Residues that contact DNA are located in the catalytic domain and in a β-hairpin loop formed by the zinc finger [5].

Endonuclease VIII (EC 3.2.-.-) (gene nei) is a DNA N-glycosylase with an AP lyase activity. It is evolutionary related to FPG. Orthologs of FPG have also been discovered in mammals (NEIL1, 2 AND 3). NEILs are also active in excising a variety of oxidatively damaged bases but show significant differences in substrate preference [6].

We have developed a signature pattern that covers the four conserved cysteines of the zinc finger, and, two profiles that span the entire catalytic domain and zinc finger.


NEIL1 proteins don't have the zinc finger motif.

Last update:

April 2006 / Pattern revised.


Technical section

PROSITE methods (with tools and information) covered by this documentation:

FPG_CAT, PS51068; Formamidopyrimidine-DNA glycosylase catalytic domain profile  (MATRIX)

ZF_FPG_2, PS51066; Zinc finger FPG-type profile  (MATRIX)

ZF_FPG_1, PS01242; Zinc finger FPG-type signature  (PATTERN)


1AuthorsFromme J.C. Verdine G.L.
TitleBase excision repair.
SourceAdv. Protein Chem. 69:1-41(2004).
PubMed ID15588838

2AuthorsDuwat P. de Oliveira R. Ehrlich S.D. Boiteux S.
TitleRepair of oxidative DNA damage in gram-positive bacteria: the Lactococcus lactis Fpg protein.
SourceMicrobiology 141:411-417(1995).
PubMed ID7704272

3AuthorsFromme J.C. Banerjee A. Verdine G.L.
TitleDNA glycosylase recognition and catalysis.
SourceCurr. Opin. Struct. Biol. 14:43-49(2004).
PubMed ID15102448

4AuthorsGilboa R. Zharkov D.O. Golan G. Fernandes A.S. Gerchman S.E. Matz E. Kycia J.H. Grollman A.P. Shoham G.
TitleStructure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA.
SourceJ. Biol. Chem. 277:19811-19816(2002).
PubMed ID11912217

5AuthorsFromme J.C. Verdine G.L.
TitleStructural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM.
SourceNat. Struct. Biol. 9:544-552(2002).
PubMed ID12055620

6AuthorsBandaru V. Sunkara S. Wallace S.S. Bond J.P.
TitleA novel human DNA glycosylase that removes oxidative DNA damage and is homologous to Escherichia coli endonuclease VIII.
SourceDNA Repair 1:517-529(2002).
PubMed ID12509226

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