DNA cytosine methyltransferases regulate the expression of the genome through the precise epigenetic marking of certain cytosines with a methyl group, and aberrant methylation is a hallmark of human diseases including cancer. Targeting these enzymes for drug design is currently a high priority.

Aug 9, 2019 · In this study, we investigated the catalytic mechanism of 3mC generation by DNMT3A. We generated several mutant enzymes with amino acid exchanges in the catalytic center and studied their ability to methylate cytosine at the C5 and N3 positions.

Cytosine residues (2) in DNA can undergo hydrolytic deamination to yield uracil residues 3 (24–28). The reaction may proceed either via attack of hydroxide on the neutral nucleobase or attack of water on the N3-protonated base ( Scheme 2 ) ( 24 , 25 , 29 ).

The N3 protonation or its absence reflects in the C2-N3-C4 bond angle. The N3 protonation in CytH+ is consistent with the larger C2-N3-C4 bond angle, 122.5 (3)°, while for unprotonated Cyt the angle is 121.1 (3)°.

Dec 24, 2019 · Of the canonical nucleobases, N3 protonation of cytosine (C) is the most widely utilized in both biology and nanotechnology. Naturally occurring C derivatives that shift the N3 p K a introduce an additional level of tunability.

Aug 1, 2022 · The N3 of cytosine is H-bonded to Wat-330 at a distance of 2.89 Å. Wat-353 is H-bonded to H5 at 2.45 Å, and Wat-340 is H-bonded to O2 of cytosine at 1.64 Å (see Fig. 1 for details). A number of reaction schemes that take one, two and three water molecules into account, were investigated in our studies.

Nov 24, 1998 · It seems likely that in the DNA (cytosine-5)-methyltransferase-catalyzed cytosine methylation proton transfers take place between Glu119 of the active site and N3 of the cytosine. The implications of the model calculations for the DNA (cytosine-5)-methyltransferase-catalyzed reactions are discussed.

May 11, 2017 · The cytosine nucleobases of the stable N3 and O2 protonated cytosine nucleosides populated in the experiments are exclusively anti oriented, and stabilized by a noncanonical C6H···O5' hydrogen-bonding interaction.

The Cys-1226 residue nucleophilically attacks the C6 on cytosine, causing double bonds in the ring to rotate, eventually leading to a proton transfer between the Glu-1266 residue and N3 on cytosine. The cofactor SAM enters the active site.

Experimental analyses using ultrasensitive liquid chromatography/mass spectrometry (LC/MS) have unambiguously confirmed that DNMT can catalyze the methylation at the N3 position of cytosine with S-adenosyl-L-methionine (AdoMet). This finding reflects that the generation of 3mC is a general reactivity enabled by cytosine methyltransferases [1].