Summary: Formamidopyrimidine-DNA glycosylase H2TH domain
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H2TH domain Edit Wikipedia article
crystal structure complex between the lactococcus lactis fpg (mutm) and a fapy-dg containing dna
In molecular biology, the H2TH domain (helix-2turn-helix domain) is a 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 EC 3.2.2.- and AP lyase activity EC 184.108.40.206. 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 220.127.116.11) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity;EC 18.104.22.168). 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. The two DNA-binding motifs (a zinc finger and the H2TH (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. 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 (EC 3.2.2.-,EC 22.214.171.124), but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine. 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 (see PDB:1K82). 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.
- Fromme JC, Verdine GL (2004). "Base excision repair". Adv. Protein Chem. 69: 1–41. doi:10.1016/S0065-3233(04)69001-2. PMID 15588838.
- Sugahara M, Mikawa T, Kumasaka T, Yamamoto M, Kato R, Fukuyama K, Inoue Y, Kuramitsu S (August 2000). "Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile, Thermus thermophilus HB8". EMBO J. 19 (15): 3857–69. doi:10.1093/emboj/19.15.3857. PMC . PMID 10921868.
- O'Connor TR, Graves RJ, de Murcia G, Castaing B, Laval J (April 1993). "Fpg protein of Escherichia coli is a zinc finger protein whose cysteine residues have a structural and/or functional role". J. Biol. Chem. 268 (12): 9063–70. PMID 8473347.
- Duwat P, de Oliveira R, Ehrlich SD, Boiteux S (February 1995). "Repair of oxidative DNA damage in gram-positive bacteria: the Lactococcus lactis Fpg protein". Microbiology. 141 (2): 411–7. doi:10.1099/13500872-141-2-411. PMID 7704272.
- Doublie S, Bandaru V, Bond JP, Wallace SS (July 2004). "The crystal structure of human endonuclease VIII-like 1 (NEIL1) reveals a zincless finger motif required for glycosylase activity". Proc. Natl. Acad. Sci. U.S.A. 101 (28): 10284–9. doi:10.1073/pnas.0402051101. PMC . PMID 15232006.
- Gilboa R, Zharkov DO, Golan G, Fernandes AS, Gerchman SE, Matz E, Kycia JH, Grollman AP, Shoham G (May 2002). "Structure of formamidopyrimidine-DNA glycosylase covalently complexed to DNA". J. Biol. Chem. 277 (22): 19811–6. doi:10.1074/jbc.M202058200. PMID 11912217.
- Fromme JC, Verdine GL (July 2002). "Structural insights into lesion recognition and repair by the bacterial 8-oxoguanine DNA glycosylase MutM". Nat. Struct. Biol. 9 (7): 544–52. doi:10.1038/nsb809. PMID 12055620.
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Formamidopyrimidine-DNA glycosylase H2TH domain Provide feedback
Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidised purines from damaged DNA. This family is the central domain containing the DNA-binding helix-two turn-helix domain .
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:||Fapy_DNA_glyco NFACT_N Ribosomal_S13|
|Similarity to PfamA using HHSearch:||NFACT_N|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR015886
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 [ 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 ].
This entry represents the central domain containing the DNA-binding helix-two turn-helix domain [ PUBMED:11912217 ].
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)|
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|Number in seed:||13|
|Number in full:||12293|
|Average length of the domain:||90.80 aa|
|Average identity of full alignment:||31 %|
|Average coverage of the sequence by the domain:||30.42 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||17|
|Download:||download the raw HMM for this family|
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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 H2TH domain has been found. There are 107 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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AlphaFold Structure Predictions
The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.