Previous X-ray crystallographic studies have revealed that the catalytic domain 
of a DNA methyltransferase (Mtase) generating C5-methylcytosine bears a striking 
structural similarity to that of a Mtase generating N6-methyladenine. Guided by 
this common structure, we performed a multiple sequence alignment of 42 
amino-Mtases (N6-adenine and N4-cytosine). This comparison revealed nine 
conserved motifs, corresponding to the motifs I to VIII and X previously defined 
in C5-cytosine Mtases. The amino and C5-cytosine Mtases thus appear to be more 
closely related than has been appreciated. The amino Mtases could be divided 
into three groups, based on the sequential order of motifs, and this variation 
in order may explain why only two motifs were previously recognized in the amino 
Mtases. The Mtases grouped in this way show several other group-specific 
properties, including differences in amino acid sequence, molecular mass and DNA 
sequence specificity. Surprisingly, the N4-cytosine and N6-adenine Mtases do not 
form separate groups. These results have implications for the catalytic 
mechanisms, evolution and diversification of this family of enzymes. 
Furthermore, a comparative analysis of the S-adenosyl-L-methionine and 
adenine/cytosine binding pockets suggests that, structurally and functionally, 
they are remarkably similar to one another.