Classification of DNA methyltransferases with Profile Hidden Markov Models

DNA methyltransferases are enzymes that specifically recognize a target sequence (typically four to six bases long) on a DNA double strand. They transfer a methyl group from Sadenosyl-L-methionine to a specific position on a specific base of their target sequence. These enzymes can be divided into two major classes, according to the position methylated. Either the methyl group is transfered onto a pyrimidine ring carbon yielding C5-methylcytosine (5mC) or onto exocyclic amino nitrogens, forming either N6-methyladeneine (N6mA) or N4-methylcytosine (N4mC). With the help of structure-guided analysis T. Malone et al. [3] were able to detect nine conserved motifs, corresponding to motifs I to VIII and X previously defined in C5-cytosine methyltransferases. Based on the sequential order of these motifs it was possible to divide the amino methyltransferases into three groups (α, β, and γ), see Fig. 1.