Domain

DNA glycosylase/AP lyase, H2TH DNA-binding (IPR015886)

Short name: DNA_glyclase/AP_lyase_DNA-bd

Domain relationships

None.

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 [PMID: 15588838]. These enzymes are primarily from bacteria, and have both DNA glycosylase activity (EC:3.2.2) and AP lyase activity (EC:4.2.99.18). 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; EC:3.2.2.23) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; EC:4.2.99.18). 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 [PMID: 10921868]. 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 [PMID: 10921868]. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines [PMID: 8473347, PMID: 7704272].

Endonuclease VIII (Nei) has the same enzyme activities as Fpg above (EC:3.2.2, EC:4.2.99.18), but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [PMID: 15232006].

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 [PMID: 11912217]. 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 [PMID: 12055620].

This entry represents the central domain containing the DNA-binding helix-two turn-helix domain [PMID: 11912217].

GO terms

Biological Process

GO:0006289 nucleotide-excision repair

Molecular Function

GO:0003906 DNA-(apurinic or apyrimidinic site) lyase activity
GO:0003684 damaged DNA binding
GO:0016799 hydrolase activity, hydrolyzing N-glycosyl compounds
GO:0008270 zinc ion binding

Cellular Component

No terms assigned in this category.

Contributing signatures

Signatures from InterPro member databases are used to construct an entry.
SMART
Pfam