Cell and Molecular Biology of DNA Methyltransferase 1 - International Review of Cell and Molecular Biology - page 10

Figure 1.3 Basic chemistry of enzymatic modification of cytosine base by transfer of
methyl group. See text for details of reactions and intermediate substrates.
deprotonation at position C5. Finally, step 4 is release of the methyltransferase
by b elimination.
DNA methylation, whether de novo methylation of unmethylated DNA
or maintenance methylation of hemimethylated DNA, occurs on double-
stranded helical DNA. The highly ordered Watson-Crick base pairs form
stacks of hydrogen-bonded planar structures inside a twisted sugar-
phosphate backbone. As pointed out by Erlanson et al. (1993) , this
three-dimensional structure imposes strict steric constraints on the chemical
mechanism. Specifically, within a double-helical configuration, the
approach trajectories to modifying bonds at both 5 and 6 positions of the
cytosine base are blocked by neighboring bases, suggesting that successful
cytosine methylation could only occur with eversion of the base outside
the double helix. A number of structures of methyltransferases, or their
accessory proteins (e.g., UHRF1, which resides at the replication foci) in
the case of eukaryotic DNA methyltransferases, with double-helical DNA
have now been resolved and all of these indicate that the steric hindrance
is indeed relieved by eversion of the target unmethylated base out of the
double helix ( Arita et al., 2008; Avvakumov et al., 2008; Hashimoto
et al., 2008; Klimasauskas et al., 1994; Song et al., 2012 ). Presumably, fol-
lowing completion of the methylation reaction and release of the covalently
linked methyltransferase, the methylated base immediately returns to its
based-paired position in the double helix.
3.2. Similarities and differences in plant and animal
maintenance methyltransferases
3.2.1 Amino acid sequence alignments
There are a number of different cytosine maintenance methyltransferases in
A. thaliana , primarily distinguished by their dinucleotide or trinucleotide
sequence substrates. MET1 is the primary maintenance methyltransferase