Methyltransferase

Group of methylating enzymes

Methyltransferases are a large group of enzymes that all methylate their substrates but can be split into several subclasses based on their structural features. The most common class of methyltransferases is class I, all of which contain a Rossmann fold for binding S Adenosyl methionine (SAM). Class II methyltransferases contain a SET domain, which are exemplified by SET domain histone methyltransferases, and class III methyltransferases, which are membrane associated. Methyltransferases can also be grouped as different types utilizing different substrates in methyl transfer reactions. These types include protein methyltransferases, DNA/RNA methyltransferases, natural product methyltransferases, and non SAM dependent methyltransferases. SAM is the classical methyl donor for methyltransferases, however, examples of other methyl donors are seen in nature. The general mechanism for methyl transfer is a SN2 like nucleophilic attack where the methionine sulfur serves as the leaving group and the methyl group attached to it acts as the electrophile that transfers the methyl group to the enzyme substrate. SAM is converted to S Adenosyl homocysteine (SAH) during this process. The breaking of the SAM methyl bond and the formation of the substrate methyl bond happen nearly simultaneously. These enzymatic reactions are found in many pathways and are implicated in genetic diseases, cancer, and metabolic diseases. Another type of methyl transfer is the radical S Adenosyl methionine (SAM) which is the methylation of unactivated carbon atoms in primary metabolites, proteins, lipids, and RNA.

Methylation, as well as other epigenetic modifications, affects transcription, gene stability, and parental imprinting. It directly impacts chromatin structure and can modulate gene transcription, or even completely silence or activate genes, without mutation to the gene itself. Though the mechanisms of this genetic control are complex, hypo and hypermethylation of DNA is implicated in many diseases.

Histone methyltransferases are critical for genetic regulation at the epigenetic level. They modify mainly lysine on the ε nitrogen and the arginine guanidinium group on histone tails. Lysine methyltransferases and Arginine methyltransferases are unique classes of enzymes, but both bind SAM as a methyl donor for their histone substrates. Lysine amino acids can be modified with one, two, or three methyl groups, while Arginine amino acids can be modified with one or two methyl groups. This increases the strength of the positive charge and residue hydrophobicity, allowing other proteins to recognize methyl marks. The effect of this modification depends on the location of the modification on the histone tail and the other histone modifications around it. The location of the modifications can be partially determined by DNA sequence, as well as small non coding RNAs and the methylation of the DNA itself. Most commonly, it is histone H3 or H4 that is methylated in vertebrates. Either increased or decreased transcription of genes around the modification can occur. Increased transcription is a result of decreased chromatin condensation, while decreased transcription results from increased chromatin condensation. Methyl marks on the histones contribute to these changes by serving as sites for recruitment of other proteins that can further modify chromatin.

N alpha methyltransferases transfer a methyl group from SAM to the N terminal nitrogen on protein targets. The N terminal methionine is first cleaved by another enzyme and the X Proline Lysine consensus sequence is recognized by the methyltransferase. For all known substrates, the X amino acid is Alanine, Serine, or Proline. This reaction yields a methylated protein and SAH. Known targets of these methyltransferases in humans include RCC 1 (a regulator of nuclear transport proteins) and Retinoblastoma protein (a tumor suppressor protein that inhibits excessive cell division). RCC 1 methylation is especially important in mitosis as it coordinates the localization of some nuclear proteins in the absence of the nuclear envelope. When RCC 1 is not methylated, cell division is abnormal following the formation of extra spindle poles. The function of Retinoblastoma protein N terminal methylation is not known.

Natural product methyltransferases (NPMTs) are a diverse group of enzymes that add methyl groups to naturally produced small molecules. Like many methyltransferases, SAM is utilized as a methyl donor and SAH is produced. Methyl groups are added to S, N, O, or C atoms, and are classified by which of these atoms are modified, with O methyltransferases representing the largest class. The methylated products of these reactions serve a variety of functions, including co factors, pigments, signalling compounds, and metabolites. NPMTs can serve a regulatory role by modifying the reactivity and availability of these compounds. These enzymes are not highly conserved across different species, as they serve a more specific function in providing small molecules for specialized pathways in species or smaller groups of species. Reflective of this diversity is the variety of catalytic strategies, including general acid base catalysis, metal based catalysis, and proximity and desolvation effects not requiring catalytic amino acids. NPMTs are the most functionally diverse class of methyltransferases. Important examples of this enzyme class in humans include phenylethanolamine N methyltransferase (PNMT), which converts norepinephrine to epinephrine, and histamine N methyltransferase (HNMT), which methylates histamine in the process of histamine metabolism. Catechol O methyltransferase (COMT) degrades a class of molecules known as catcholamines that includes dopamine, epinephrine, and norepenepherine.

Methanol, methyl tetrahydrofolate, mono , di , and trimethylamine, methanethiol, methyltetrahydromethanopterin, and chloromethane are all methyl donors found in biology as methyl group donors, typically in enzymatic reactions using the cofactor vitamin B12. These substrates contribute to methyl transfer pathways including methionine biosynthesis, methanogenesis, and acetogenesis.

Recent work has revealed the methyltransferases involved in methylation of naturally occurring anticancer agents to use S Adenosyl methionine (SAM) analogs that carry alternative alkyl groups as a replacement for methyl. The development of the facile chemoenzymatic platform to generate and utilize differentially alkylated SAM analogs in the context of drug discovery and drug development is known as alkylrandomization.

In human cells, it was found that m5C was associated with abnormal tumor cells in cancer. The role and potential application of m5C includes to balance the impaired DNA in cancer both hypermethylation and hypomethylation. An epigenetic repair of DNA can be applied by changing the m5C amount in both types of cancer cells (hypermethylation/ hypomethylation) and as well as the environment of the cancers to reach an equivalent point to inhibit tumor cells.