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The x-ray crystal structure of Thermus aquaticus DNA methyltransferase M-Taq I, in complex with S-adenosylmethionine, at 2.4-angstrom resolution exhibits the alpha/beta folding of the polypeptide into two equal sized-regions. The two regions form a C with a wide cleft that can accommodate the DNA substrate. The N-terminal domain is occupied by a nine-standard beta-sheet and the C-terminal domain by four small beta-sheets and alpha-helices. The beta sheet has two conserved segments typical of N-methyltransferases, which form a pocket for cofactor binding. The three-dimensional folding of M-Taq I resembles that of the cytosine-specific Hha I methyltransferase.