5-methylcytosine catabolic process
Definition
Target type: biologicalprocess
The chemical reactions and pathways resulting in the breakdown of 5-methylcytosine, a methylated base of DNA. [GOC:go_curators]
5-Methylcytosine catabolic process is the breakdown of 5-methylcytosine (5mC), a modified base found in DNA, into its constituent components. This process is essential for DNA demethylation, a crucial regulatory mechanism involved in various cellular processes, including development, differentiation, and disease.
The catabolism of 5mC is initiated by the enzyme thymine DNA glycosylase (TDG), which removes 5mC from the DNA backbone. TDG recognizes 5mC as a damaged base and excises it, creating an abasic site. This site is then processed by the base excision repair (BER) pathway, which removes the abasic site and inserts a new cytosine base, effectively converting 5mC to cytosine.
The BER pathway involves a series of enzymes, including apurinic/apyrimidinic endonuclease 1 (APE1), DNA polymerase beta (Pol beta), and DNA ligase. APE1 cleaves the DNA backbone at the abasic site, creating a single-strand break. Pol beta then inserts a new cytosine base opposite the abasic site, and DNA ligase seals the break, restoring the DNA strand to its original sequence.
In addition to the BER pathway, other pathways have been implicated in 5mC catabolism, including the translesion synthesis pathway and the mismatch repair pathway. These pathways play a role in repairing DNA damage and maintaining genome integrity.
5-Methylcytosine catabolism is a highly regulated process, and its dysregulation can lead to various pathological conditions, including cancer, neurodevelopmental disorders, and autoimmune diseases. The understanding of 5mC catabolic process has important implications for the development of novel therapeutic strategies targeting epigenetic modifications in disease.'
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Proteins (1)
| Protein | Definition | Taxonomy |
|---|---|---|
| Methylcytosine dioxygenase TET2 | A methylcytosine dioxygenase TET2 that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q6N021] | Homo sapiens (human) |
Compounds (4)
| Compound | Definition | Classes | Roles |
|---|---|---|---|
| alpha-hydroxyglutarate | 2-hydroxyglutarate : A dicarboxylic acid anion obtained by deprotonation of at least one of the carboxy groups of 2-hydroxyglutaric acid. 2-hydroxyglutaric acid : A 2-hydroxydicarboxylic acid that is glutaric acid in which one hydrogen alpha- to a carboxylic acid group is substituted by a hydroxy group. | 2-hydroxydicarboxylic acid; dicarboxylic fatty acid | metabolite; mouse metabolite |
| deferoxamine | Deferoxamine: Natural product isolated from Streptomyces pilosus. It forms iron complexes and is used as a chelating agent, particularly in the mesylate form. desferrioxamine B : An acyclic desferrioxamine that is butanedioic acid in which one of the carboxy groups undergoes formal condensation with the primary amino group of N-(5-aminopentyl)-N-hydroxyacetamide and the second carboxy group undergoes formal condensation with the hydroxyamino group of N(1)-(5-aminopentyl)-N(1)-hydroxy-N(4)-[5-(hydroxyamino)pentyl]butanediamide. It is a siderophore native to Streptomyces pilosus biosynthesised by the DesABCD enzyme cluster as a high affinity Fe(III) chelator. | acyclic desferrioxamine | bacterial metabolite; ferroptosis inhibitor; iron chelator; siderophore |
| 5-carboxy-8-hydroxyquinoline | 5-carboxy-8-hydroxyquinoline: a JmjC histone demethylase inhibitor; structure in first source | quinolines | |
| oxalylglycine | N-oxalylglycine : An amino dicarboxylic acid that is iminodiacetic acid with an oxo substituent. It is used as an inhibitor of alpha-ketoglutarate dependent (EC 1.14.11.*) enzymes. oxalylglycine: structure given in first source | amino dicarboxylic acid; N-acylglycine | EC 1.14.11.* (oxidoreductase acting on paired donors, 2-oxoglutarate as one donor, incorporating 1 atom each of oxygen into both donors) inhibitor |