InterPro : IPR015886

Name  DNA glycosylase/AP lyase, H2TH DNA-binding Short Name  DNA_glyclase/AP_lyase_DNA-bd
Type  Domain Description  This entry represents a helix-2turn-helix DNA-binding domain found in DNA glycosylase/AP lyase enzymes, which are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. Most damage to bases in DNA is repaired by the base excision repair pathway []. These enzymes are primarily from bacteria, and have both DNA glycosylase activity () and AP lyase activity (). Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei).Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; ) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; ). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines [, ].Endonuclease VIII (Nei) has the same enzyme activities as Fpg above (, ), but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [].These 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 []. 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 beta-hairpin loop formed by the zinc finger [].This entry represents the central domain containing the DNA-binding helix-two turn-helix domain [].
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Sequence Features

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Proteins

InterPro protein domain ID --> Contigs

 

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0 Child Features

0 Contains

2 Found In

Id Name Short Name Type
IPR000191 DNA glycosylase/AP lyase DNA_glycosylase/AP_lyase Family
IPR020629 Formamidopyrimidine-DNA glycosylase Formamido-pyr_DNA_Glyclase Family

1 Parent Features

Id Name Short Name Type
IPR010979 Ribosomal protein S13-like, H2TH Ribosomal_S13-like_H2TH Domain

7 Publications

First Author Title Year Journal Volume Pages
O'Connor TR Fpg protein of Escherichia coli is a zinc finger protein whose cysteine residues have a structural and/or functional role. 1993 J Biol Chem 268 9063-70
Duwat P Repair of oxidative DNA damage in gram-positive bacteria: the Lactococcus lactis Fpg protein. 1995 Microbiology 141 ( Pt 2) 411-7
Sugahara M Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile, Thermus thermophilus HB8. 2000 EMBO J 19 3857-69
Doublié S The crystal structure of human endonuclease VIII-like 1 (NEIL1) reveals a zincless finger motif required for glycosylase activity. 2004 Proc Natl Acad Sci U S A 101 10284-9
Gilboa R Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA. 2002 J Biol Chem 277 19811-6
Fromme JC Base excision repair. 2004 Adv Protein Chem 69 1-41
Fromme JC Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM. 2002 Nat Struct Biol 9 544-52



To cite PlanMine, please refer to the following publication:

Rozanski, A., Moon, H., Brandl, H., Martín-Durán, J. M., Grohme, M., Hüttner, K., Bartscherer, K., Henry, I., & Rink, J. C.
PlanMine 3.0—improvements to a mineable resource of flatworm biology and biodiversity
Nucleic Acids Research, gky1070. doi:10.1093/nar/gky1070 (2018)