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IPR012319

Source: InterPro

Description

IPR012319 is a Formamidopyrimidine-DNA glycosylase, catalytic domain.

<p>This entry represents the catalytic domain of DNA glycosylase/AP lyase enzymes including formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei).</p> <p>Formamidopyrimidine-DNA glycosylases (Fpg, MutM) are trifunctional DNA base excision repair enzymes that remove a wide range of oxidation-damaged bases (N-glycosylase activity; [ec:3.2.2.23]) and cleave 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 oxidised 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 [[cite:PUB00014010]]. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidised 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 [[cite:PUB00014010]]. Fpg binds one ion of zinc at the C-terminal, which contains four conserved and essential cysteines [[cite:PUB00002832], [cite:PUB00003593]].</p> <p>Endonuclease VIII (Nei) has the same enzyme activities as Fpg ([ec:3.2.2], [ec:4.2.99.18]), but with a preference for oxidised pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [[cite:PUB00031419]]. These proteins contain three structural domains: an N-terminal catalytic core domain, a central helix-two turn-helix (H2TH) module and a C-terminal zinc finger [[cite:PUB00012853]]. 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 [[cite:PUB00018047]].</p>

This description is obtained from EB-eye REST.

Associated GO terms

GO predictions are based solely on the InterPro-to-GO mappings published by EMBL-EBI, which are in turn based on the mapping of predicted domains to the InterPro dataset. The InterPro-to-GO mapping was last updated on , while the GO metadata was last updated on .

GO term Namespace Name Definition Relationships
GO:0003684
Molecular function Damaged DNA binding Interacting selectively and non-covalently with damaged DNA.
Subterm of
GO:0003906
Molecular function DNA-(apurinic or apyrimidinic site) endonuclease activity Catalysis of the cleavage of the C-O-P bond in the AP site created when DNA glycosylase removes a damaged base, involved in the DNA base excision repair pathway (BER).
Subterm of
GO:0006284
Biological process Base-excision repair In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
Subterm of
GO:0008270
Molecular function Zinc ion binding Interacting selectively and non-covalently with zinc (Zn) ions.
Subterm of
GO:0016799
Molecular function Hydrolase activity, hydrolyzing N-glycosyl compounds Catalysis of the hydrolysis of any N-glycosyl bond.
Subterm of

Associated Lotus transcripts 5

Transcript Name Description Predicted domains Domain count
Lj3g3v0044230.1
– PREDICTED: formamidopyrimidine-DNA glycosylase-like isoform X2 [Cicer arietinum] gi|502080701|ref|XP_004486650.1|
Domains
18
Lj3g3v0044230.2
– PREDICTED: formamidopyrimidine-DNA glycosylase-like isoform X1 [Cicer arietinum] gi|502080698|ref|XP_004486649.1|
Domains
18
LotjaGi3g1v0007500.1
– Formamidopyrimidine-DNA glycosylase; TAIR: AT1G52500.2 MUTM homolog-1; Swiss-Prot: sp|O80358|FPG_ARATH Formamidopyrimidine-DNA glycosylase; TrEMBL-Plants: tr|A0A151SPP2|A0A151SPP2_CAJCA Formamidopyrimidine-DNA glycosylase; Found in the gene: LotjaGi3g1v0007500
Domains
19
LotjaGi3g1v0007500.2
– Formamidopyrimidine-DNA glycosylase; TAIR: AT1G52500.2 MUTM homolog-1; Swiss-Prot: sp|O80358|FPG_ARATH Formamidopyrimidine-DNA glycosylase; TrEMBL-Plants: tr|G7II90|G7II90_MEDTR Formamidopyrimidine-DNA glycosylase; Found in the gene: LotjaGi3g1v0007500
Domains
19
LotjaGi3g1v0007500.3
– Formamidopyrimidine-DNA glycosylase; TAIR: AT1G52500.1 MUTM homolog-1; Swiss-Prot: sp|O80358|FPG_ARATH Formamidopyrimidine-DNA glycosylase; TrEMBL-Plants: tr|A0A151SPP2|A0A151SPP2_CAJCA Formamidopyrimidine-DNA glycosylase; Found in the gene: LotjaGi3g1v0007500
Domains
18

Co-occuring domains 1

A list of co-occurring predicted domains within the L. japonicus gene space:

Predicted domain Source Observations Saturation (%)
cd08972 CDD 1 20.00