H2TH domain
Encyclopedia
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 enzyme
s 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 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 cysteine
s.
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 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. Residue
s that contact DNA are located in the catalytic
domain and in a beta-hairpin loop
formed by the zinc finger.
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
-binding domain
Protein domain
A protein domain is a part of protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded. Many proteins consist of several structural...
found in DNA glycosylase/AP lyase
DNA-(apurinic or apyrimidinic site) lyase
In enzymology, a DNA- lyase is an enzyme that catalyzes the chemical reactionThis enzyme belongs to the family of lyases, specifically the "catch-all" class of lyases that cleave carbon-oxygen bonds. The systematic name of this enzyme class is DNA- 5'-phosphomonoester-lyase...
enzymes, which are involved in base excision repair
Base excision repair
In biochemistry and genetics, base excision repair is a cellular mechanism that repairs damaged DNA throughout the cell cycle. It is responsible primarily for removing small, non-helix-distorting base lesions from the genome. The related nucleotide excision repair pathway repairs bulky...
of DNA damaged by oxidation
Redox
Redox reactions describe all chemical reactions in which atoms have their oxidation state changed....
or by mutagenic agents. Most damage to bases
Nucleotide
Nucleotides are molecules that, when joined together, make up the structural units of RNA and DNA. In addition, nucleotides participate in cellular signaling , and are incorporated into important cofactors of enzymatic reactions...
in DNA is repaired
DNA repair
DNA repair refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as UV light and radiation can cause DNA damage, resulting in as many as 1...
by the base excision repair pathway. These enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
s are primarily from bacteria, and have both DNA glycosylase activity and AP lyase activity . Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease
Endonuclease
Endonucleases are enzymes that cleave the phosphodiester bond within a polynucleotide chain, in contrast to exonucleases, which cleave phosphodiester bonds at the end of a polynucleotide chain. Typically, a restriction site will be a palindromic sequence four to six nucleotides long. Most...
VIII (Nei).
Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases
Base pair
In molecular biology and genetics, the linking between two nitrogenous bases on opposite complementary DNA or certain types of RNA strands that are connected via hydrogen bonds is called a base pair...
(N-glycosylase activity; ) and cleaves
Cleavage
Cleavage may refer to:*Cleavage , partial exposure of the separation between a woman's breasts.**Cleavage enhancement, methods of making a person's breast cleavage look more substantial than it really is....
both the 3'- and 5'-phosphodiester bonds
Phosphodiester bond
A phosphodiester bond is a group of strong covalent bonds between a phosphate group and two 5-carbon ring carbohydrates over two ester bonds. Phosphodiester bonds are central to all known life, as they make up the backbone of each helical strand of DNA...
of the resulting apurinic/apyrimidinic site (AP lyase activity;). 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
Monomer
A monomer is an atom or a small molecule that may bind chemically to other monomers to form a polymer; the term "monomeric protein" may also be used to describe one of the proteins making up a multiprotein complex...
composed of 2 domains
Protein domain
A protein domain is a part of protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded. Many proteins consist of several structural...
connected by a flexible hinge. The two DNA-binding motifs (a zinc finger
Zinc finger
Zinc fingers are small protein structural motifs that can coordinate one or more zinc ions to help stabilize their folds. They can be classified into several different structural families and typically function as interaction modules that bind DNA, RNA, proteins, or small molecules...
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
Catalysis
Catalysis is the change in rate of a chemical reaction due to the participation of a substance called a catalyst. Unlike other reagents that participate in the chemical reaction, a catalyst is not consumed by the reaction itself. A catalyst may participate in multiple chemical transformations....
similar to that of bifunctional base excision repair enzymes. Fpg binds one ion
Ion
An ion is an atom or molecule in which the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge. The name was given by physicist Michael Faraday for the substances that allow a current to pass between electrodes in a...
of zinc
Zinc
Zinc , or spelter , is a metallic chemical element; it has the symbol Zn and atomic number 30. It is the first element in group 12 of the periodic table. Zinc is, in some respects, chemically similar to magnesium, because its ion is of similar size and its only common oxidation state is +2...
at the C terminus, which contains four conserved
Conserved sequence
In biology, conserved sequences are similar or identical sequences that occur within nucleic acid sequences , protein sequences, protein structures or polymeric carbohydrates across species or within different molecules produced by the same organism...
and essential cysteine
Cysteine
Cysteine is an α-amino acid with the chemical formula HO2CCHCH2SH. It is a non-essential amino acid, which means that it is biosynthesized in humans. Its codons are UGU and UGC. The side chain on cysteine is thiol, which is polar and thus cysteine is usually classified as a hydrophilic amino acid...
s.
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
Dihydrouracil
Dihydrouracil is an intermediate in the catabolism of uracil.-See also:* Dihydrouracil dehydrogenase * Dihydrouracil oxidase* Dihydropyrimidinase...
and 5,6-dihydrothymine
Dihydrothymine
Dihydrothymine is an intermediate in the metabolism of thymine....
. These proteins contain three structural
Secondary structure
In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...
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
Biocatalysis
Biocatalysis is the use of natural catalysts, such as protein enzymes, to perform chemical transformations on organic compounds. Both enzymes that have been more or less isolated and enzymes still residing inside living cells are employed for this task....
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. Residue
Residue
Residue may refer to:* Residue , material remaining after a distillation or an evaporation, or portion of a larger molecule** In particular, in biology, often refers specifically to an amino acid...
s that contact DNA are located in the catalytic
Catalysis
Catalysis is the change in rate of a chemical reaction due to the participation of a substance called a catalyst. Unlike other reagents that participate in the chemical reaction, a catalyst is not consumed by the reaction itself. A catalyst may participate in multiple chemical transformations....
domain and in a beta-hairpin loop
Turn (biochemistry)
A turn is an element of secondary structure in proteins where the polypeptide chain reverses its overall direction.- Definition :According to the most common definition, a turn is a structural motif where the Cα atoms of two residues separated by few peptide bonds are in close approach A turn is...
formed by the zinc finger.