single-stranded DNA 3'-5' DNA exonuclease activity
Definition
Target type: molecularfunction
Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a single-stranded DNA molecule. [GOC:mah, PMID:22562358]
Single-stranded DNA 3'-5' exonuclease activity is a catalytic process that involves the removal of nucleotides from the 3' end of a single-stranded DNA molecule. This activity is essential for a variety of cellular processes, including DNA replication, repair, and recombination. During DNA replication, exonucleases can remove mismatched nucleotides that are incorporated into the newly synthesized DNA strand. This ensures that the replicated DNA is faithful to the original template. In DNA repair, exonucleases can remove damaged nucleotides from the DNA strand, allowing for the synthesis of a new, undamaged strand. Finally, in DNA recombination, exonucleases can remove nucleotides from the ends of broken DNA molecules, allowing for the rejoining of the broken strands. The mechanism of single-stranded DNA 3'-5' exonuclease activity involves the binding of the exonuclease to the DNA substrate. The exonuclease then cleaves the phosphodiester bond between the 3' hydroxyl group of the penultimate nucleotide and the 5' phosphate group of the terminal nucleotide. This process releases the terminal nucleotide and generates a new 3' hydroxyl group that can serve as a substrate for further exonucleolytic cleavage. The specificity of single-stranded DNA 3'-5' exonucleases for single-stranded DNA is due to the presence of a binding site that recognizes and interacts with the single-stranded DNA backbone. This binding site typically consists of positively charged amino acid residues that interact with the negatively charged phosphate groups of the DNA backbone. The exonucleases also exhibit a preference for the 3' end of the DNA molecule, which is dictated by the orientation of the catalytic site. The catalytic site is typically located near the 3' end of the DNA molecule, allowing for the efficient cleavage of the phosphodiester bond between the 3' hydroxyl group and the 5' phosphate group. Single-stranded DNA 3'-5' exonuclease activity is a critical component of DNA metabolism. The activity of these enzymes is tightly regulated to ensure that the appropriate amount of exonucleolytic activity occurs in the cell. In addition to their role in DNA replication, repair, and recombination, single-stranded DNA 3'-5' exonucleases are also involved in other cellular processes, such as the regulation of gene expression and the degradation of viral DNA.'
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Proteins (2)
| Protein | Definition | Taxonomy |
|---|---|---|
| Ribonuclease T | A ribonuclease T that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P30014] | Escherichia coli K-12 |
| DNA polymerase subunit gamma-1 | A DNA polymerase subunit gamma-1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P54098] | Homo sapiens (human) |
Compounds (8)
| Compound | Definition | Classes | Roles |
|---|---|---|---|
| citric acid, anhydrous | citric acid : A tricarboxylic acid that is propane-1,2,3-tricarboxylic acid bearing a hydroxy substituent at position 2. It is an important metabolite in the pathway of all aerobic organisms. Citric Acid: A key intermediate in metabolism. It is an acid compound found in citrus fruits. The salts of citric acid (citrates) can be used as anticoagulants due to their calcium chelating ability. | tricarboxylic acid | antimicrobial agent; chelator; food acidity regulator; fundamental metabolite |
| aurintricarboxylic acid | aurintricarboxylic acid : A member of the class of quinomethanes that is 3-methylidene-6-oxocyclohexa-1,4-diene-1-carboxylic acid in which the methylidene hydrogens are replaced by 4-carboxy-3-hydroxyphenyl groups. The trisodium salt is the biological stain 'chrome violet CG' while the triammonium salt is 'aluminon'. Aurintricarboxylic Acid: A dye which inhibits protein biosynthesis at the initial stages. The ammonium salt (aluminon) is a reagent for the colorimetric estimation of aluminum in water, foods, and tissues. | monohydroxybenzoic acid; quinomethanes; tricarboxylic acid | fluorochrome; histological dye; insulin-like growth factor receptor 1 antagonist |
| dithionitrobenzoic acid | dithionitrobenzoic acid : An organic disulfide that results from the formal oxidative dimerisation of 2-nitro-5-thiobenzoic acid. An indicator used to quantify the number or concentration of thiol groups. Dithionitrobenzoic Acid: A standard reagent for the determination of reactive sulfhydryl groups by absorbance measurements. It is used primarily for the determination of sulfhydryl and disulfide groups in proteins. The color produced is due to the formation of a thio anion, 3-carboxyl-4-nitrothiophenolate. | nitrobenzoic acid; organic disulfide | indicator |
| 7-nitro-1h-indole-2-carboxylic acid | 7-nitro-1H-indole-2-carboxylic acid: acts on AP endonuclease, 3'-phosphodiesterase, and 3'-phosphatase activities of APE1; structure in first source | ||
| TTP | pyrimidine ribonucleoside 5'-triphosphate | ||
| aphidicolin | aphidicolin : A tetracyclic diterpenoid that has an tetradecahydro-8,11a-methanocyclohepta[a]naphthalene skeleton with two hydroxymethyl substituents at positions 4 and 9, two methyl substituents at positions 4 and 11b and two hydroxy substituents at positions 3 and 9. An antibiotic with antiviral and antimitotical properties. Aphidicolin is a reversible inhibitor of eukaryotic nuclear DNA replication. Aphidicolin: An antiviral antibiotic produced by Cephalosporium aphidicola and other fungi. It inhibits the growth of eukaryotic cells and certain animal viruses by selectively inhibiting the cellular replication of DNA polymerase II or the viral-induced DNA polymerases. The drug may be useful for controlling excessive cell proliferation in patients with cancer, psoriasis or other dermatitis with little or no adverse effect upon non-multiplying cells. | tetracyclic diterpenoid | antimicrobial agent; antimitotic; antineoplastic agent; antiviral drug; apoptosis inducer; Aspergillus metabolite; DNA synthesis inhibitor; EC 2.7.7.7 (DNA-directed DNA polymerase) inhibitor; fungal metabolite |
| deoxyguanosine triphosphate | deoxyguanosine phosphate; guanyl deoxyribonucleotide; purine 2'-deoxyribonucleoside 5'-triphosphate | Arabidopsis thaliana metabolite; Escherichia coli metabolite; human metabolite; mouse metabolite; plant metabolite; Saccharomyces cerevisiae metabolite | |
| acyclovir triphosphate |