Summary: Formamidopyrimidine-DNA glycosylase N-terminal domain
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Formamidopyrimidine-DNA glycosylase N-terminal domain Provide feedback
Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidised purines from damaged DNA. This family is the N-terminal domain contains eight beta-strands, forming a beta-sandwich with two alpha-helices parallel to its edges [1].
Literature references
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Gilboa R, Zharkov DO, Golan G, Fernandes AS, Gerchman SE, Matz E, Kycia JH, Grollman AP, Shoham G; , J Biol Chem 2002;277:19811-19816.: Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA. PUBMED:11912217 EPMC:11912217
Internal database links
SCOOP: | H2TH |
External database links
PROSITE: | PDOC00956 |
SCOP: | 1k82 |
This tab holds annotation information from the InterPro database.
InterPro entry IPR012319
This entry represents the catalytic domain of 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 [PUBMED:15588838]. These enzymes are primarily from bacteria, and have both DNA glycosylase activity (EC) and AP lyase activity (EC). 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) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; EC). 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 [PUBMED: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 [PUBMED:10921868]. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines [PUBMED:8473347, PUBMED:7704272].
Endonuclease VIII (Nei) has the same enzyme activities as Fpg above (EC, EC), but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [PUBMED: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 [PUBMED: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 [PUBMED:12055620].
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | DNA-(apurinic or apyrimidinic site) endonuclease activity (GO:0003906) |
hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799) | |
damaged DNA binding (GO:0003684) | |
zinc ion binding (GO:0008270) | |
Biological process | base-excision repair (GO:0006284) |
Domain organisation
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Alignments
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Seed (820) |
Full (9797) |
Representative proteomes | UniProt (26585) |
NCBI (35945) |
Meta (2216) |
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RP15 (2198) |
RP35 (6355) |
RP55 (9930) |
RP75 (14039) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (820) |
Full (9797) |
Representative proteomes | UniProt (26585) |
NCBI (35945) |
Meta (2216) |
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RP15 (2198) |
RP35 (6355) |
RP55 (9930) |
RP75 (14039) |
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Raw Stockholm | |||||||||
Gzipped |
You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.
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Curation and family details
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Curation
Seed source: | Prosite |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
Number in seed: | 820 |
Number in full: | 9797 |
Average length of the domain: | 121.60 aa |
Average identity of full alignment: | 27 % |
Average coverage of the sequence by the domain: | 42.20 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 116 | ||||||||||||
Family (HMM) version: | 24 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
Structures
For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Fapy_DNA_glyco domain has been found. There are 108 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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