DNA-methyltransferase activity
Definition
Target type: molecularfunction
Catalysis of the transfer of a methyl group to a DNA molecule. [GOC:jl, ISBN:0198506732, PMID:7862522]
DNA methyltransferases (DNMTs) are a family of enzymes that catalyze the transfer of a methyl group from a donor molecule, typically S-adenosyl methionine (SAM), to a cytosine base in DNA. This process, known as DNA methylation, is a crucial epigenetic modification that plays a vital role in regulating gene expression, genomic stability, and development.
The mechanism of DNA methylation by DNMTs involves several key steps:
1. **Binding to DNA:** DNMTs recognize and bind to specific DNA sequences, often CpG dinucleotides, which are regions where a cytosine base is followed by a guanine base.
2. **SAM Binding:** DNMTs bind to SAM, the methyl group donor.
3. **Catalyzing Methyl Transfer:** The active site of DNMTs positions the cytosine base in the DNA and the methyl group from SAM in close proximity, facilitating the transfer of the methyl group to the 5' position of the cytosine base.
4. **Product Release:** After methylation, the DNMTs release the methylated DNA and the demethylated SAM.
The methylation of cytosine bases can have diverse effects on gene expression, depending on the location and context of the modification:
* **Gene Silencing:** Methylation of CpG islands within gene promoters often leads to gene silencing by preventing the binding of transcription factors and promoting the recruitment of repressive chromatin remodeling complexes.
* **Gene Activation:** In certain contexts, methylation can also enhance gene expression. For example, methylation within gene bodies can enhance transcription elongation and stability.
* **Genomic Stability:** DNA methylation contributes to genomic stability by protecting DNA from transposon activation and preventing aberrant recombination events.
* **Development:** DNA methylation plays a crucial role in development, influencing cell differentiation, tissue specialization, and embryonic development.
DNA methylation patterns are dynamic and can be influenced by various factors, including environmental stimuli, developmental cues, and aging. Dysregulation of DNA methylation is associated with several diseases, including cancer, neurodevelopmental disorders, and autoimmune disorders.
Overall, DNA methyltransferase activity is a fundamental enzymatic process that plays a critical role in regulating gene expression, genomic stability, and development. The precise role of DNA methylation in these processes is complex and highly context-dependent.'
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Proteins (3)
| Protein | Definition | Taxonomy |
|---|---|---|
| DNA (cytosine-5)-methyltransferase 3B | A DNA (cytosine-5)-methyltransferase 3B that is encoded in the genome of human. [PRO:DNx, UniProtKB:Q9UBC3] | Homo sapiens (human) |
| DNA (cytosine-5)-methyltransferase 1 | A DNA (cytosine-5)-methyltransferase 1 that is encoded in the genome of human. [PRO:DNx, UniProtKB:P26358] | Homo sapiens (human) |
| Methylated-DNA--protein-cysteine methyltransferase | A methylated-DNA--protein-cysteine methyltransferase that is encoded in the genome of human. [PRO:DNx, UniProtKB:P16455] | Homo sapiens (human) |
Compounds (30)
| Compound | Definition | Classes | Roles |
|---|---|---|---|
| nu2058 | NU2058: structure in first source | ||
| o(6)-benzylguanine | O(6)-benzylguanine: a suicide inhibitor of O(6)-methylguanine-DNA methyltransferase activity | ||
| procainamide | procainamide : A benzamide that is 4-aminobenzamide substituted on the amide N by a 2-(diethylamino)ethyl group. It is a pharmaceutical antiarrhythmic agent used for the medical treatment of cardiac arrhythmias. Procainamide: A class Ia antiarrhythmic drug that is structurally-related to PROCAINE. | benzamides | anti-arrhythmia drug; platelet aggregation inhibitor; sodium channel blocker |
| vorinostat | vorinostat : A dicarboxylic acid diamide comprising suberic (octanedioic) acid coupled to aniline and hydroxylamine. A histone deacetylase inhibitor, it is marketed under the name Zolinza for the treatment of cutaneous T cell lymphoma (CTCL). Vorinostat: A hydroxamic acid and anilide derivative that acts as a HISTONE DEACETYLASE inhibitor. It is used in the treatment of CUTANEOUS T-CELL LYMPHOMA and SEZARY SYNDROME. | dicarboxylic acid diamide; hydroxamic acid | antineoplastic agent; apoptosis inducer; EC 3.5.1.98 (histone deacetylase) inhibitor |
| dichlone | dichlone: structure | ||
| azacitidine | 5-azacytidine : An N-glycosyl-1,3,5-triazine that is 4-amino-1,3,5-triazin-2(1H)-one substituted by a beta-D-ribofuranosyl residue via an N-glycosidic linkage. An antineoplastic agent, it is used in the treatment of myeloid leukaemia. Azacitidine: A pyrimidine analogue that inhibits DNA methyltransferase, impairing DNA methylation. It is also an antimetabolite of cytidine, incorporated primarily into RNA. Azacytidine has been used as an antineoplastic agent. | N-glycosyl-1,3,5-triazine; nucleoside analogue | antineoplastic agent |
| epigallocatechin gallate | (-)-epigallocatechin 3-gallate : A gallate ester obtained by the formal condensation of gallic acid with the (3R)-hydroxy group of (-)-epigallocatechin. epigallocatechin gallate: a steroid 5alpha-reductase inhibitor and antimutagen in green tea (Camellia sinensis) | flavans; gallate ester; polyphenol | antineoplastic agent; antioxidant; apoptosis inducer; geroprotector; Hsp90 inhibitor; neuroprotective agent; plant metabolite |
| o-(6)-methylguanine | 6-O-methylguanine : A methylguanine in which the methyl group is positioned on the oxygen at position 6. Formed in DNA by alkylation of the oxygen atom of guanine, most often by N-nitroso compounds and sometimes due to methylation by other compounds such as endogenous S-adenosylmethionine, it base-pairs to thymine rather than cytidine, causing a G:C to A:T transition in DNA. methylguanine : A 2-aminopurine that is guanine bearing a single methyl substituent. O-(6)-methylguanine: structure | methylguanine | mutagen |
| 5,5'-methylenedisalicylic acid | 5,5'-methylenedisalicylic acid: inhibits attachment of ribosomes to microsomal membranes; RN given refers to parent cpd; structure in first source & Merck Index, 9th ed, #5934 | ||
| o(6)-n-butylguanine | |||
| 6-ethylguanine | 6-ethylguanine: found in rat brain DNA | ||
| s-tubercidinylhomocysteine | |||
| o(6)-benzyl-2'-deoxyguanosine | |||
| 6-bromo-3-(bromomethyl)-7-methyl-2,3,7-trichloro-1-octene | 6-bromo-3-(bromomethyl)-7-methyl-2,3,7-trichloro-1-octene: structure given in first source | monoterpenoid; organobromine compound; organochlorine compound | algal metabolite; antineoplastic agent; marine metabolite |
| s-adenosyl-3-thiopropylamine | S-adenosyl-3-thiopropylamine : A thioadenosine that is adenosine in which the hydroxy group at C-5' is replaced by a 3-aminopropyl group. S-adenosyl-3-thiopropylamine: decarboxylated S-adenosylhomocysteine; RN given refers to parent cpd | organic sulfide; primary amino compound; thioadenosine | |
| 2,4-diamino-6-benzyloxy-5-nitrosopyrimidine | 2,4-diamino-6-benzyloxy-5-nitrosopyrimidine: inhibits O(6)-alkylguanine-DNA alkyltransferase; structure given in first source | ||
| n(4)-adenosyl-n(4)-methyl-2,4-diaminobutanoic acid | |||
| nsc 401077 | NSC 401077: inhibits DNA methyltransferase DNMT1; structure in first source | ||
| s-adenosylhomocysteine | S-adenosyl-L-homocysteine : An organic sulfide that is the S-adenosyl derivative of L-homocysteine. S-Adenosylhomocysteine: 5'-S-(3-Amino-3-carboxypropyl)-5'-thioadenosine. Formed from S-adenosylmethionine after transmethylation reactions. | adenosines; amino acid zwitterion; homocysteine derivative; homocysteines; organic sulfide | cofactor; EC 2.1.1.72 [site-specific DNA-methyltransferase (adenine-specific)] inhibitor; EC 2.1.1.79 (cyclopropane-fatty-acyl-phospholipid synthase) inhibitor; epitope; fundamental metabolite |
| nanaomycin a | nanaomycin A : A pyranonaphthoquinone antibiotic from strain OS-3966 of Streptomyces rosa var. notoensis. nanaomycin A: produced by a strain OS-3966 of Streptomyces rosa var. notoensis; quinone-related cpd; MF C16-H14-O6; see also nanaomycin B: 52934-85-7, nanaomycin C: 58286-55-8, nanaomycin E: 72660-52-7; structure | benzoisochromanequinone; monocarboxylic acid; organooxygen heterocyclic antibiotic; p-quinones | bacterial metabolite |
| decitabine | 2'-deoxyribonucleoside | ||
| rg108 | RG108: DNA methyltransferase inhibitor; structure in first source | indolyl carboxylic acid | |
| lomeguatrib | |||
| genistein | 7-hydroxyisoflavones | antineoplastic agent; EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor; geroprotector; human urinary metabolite; phytoestrogen; plant metabolite; tyrosine kinase inhibitor | |
| psammaplin a | psammaplin A: isolated from marine sponges Poecillastra and Jaspis; structure in second source | ||
| sgi-1027 | SGI-1027: inhibits DNA methyltransferase 1; structure in first source | ||
| bix 01294 | piperidines | ||
| unc 0638 | UNC 0638: inhibits lysine methyltransferases G9a and GLP; structure in first source | quinazolines | |
| gsk343 | GSK343 : A member of the class of indazoles that is 1-isopropyl-1H-indazole-4-carboxamide in which the nitrogen of the carboxamide group is substituted by a (6-methyl-2-oxo-4-propyl-1,2-dihydropyridin-3-yl)methyl group and in which the indazole ring is substituted at position 6 by a 2-(4-methylpiperazin-1-yl)pyridin-4-yl group. A highly potent and selective EZH2 inhibitor (IC50 = 4 nM). GSK343: an EZH2 methyltransferase inhibitor | aminopyridine; indazoles; N-alkylpiperazine; N-arylpiperazine; pyridone; secondary carboxamide | antineoplastic agent; apoptosis inducer; EC 2.1.1.43 (enhancer of zeste homolog 2) inhibitor |
| 6,7-dimethoxy-2-(pyrrolidin-1-yl)-n-(5-(pyrrolidin-1-yl)pentyl)quinazolin-4-amine | 6,7-dimethoxy-2-(pyrrolidin-1-yl)-N-(5-(pyrrolidin-1-yl)pentyl)quinazolin-4-amine: a SETD8 inhibitor; structure in first source |