The first three-dimensional structure of a DNA methyltransferase is presented. The crystal structure of the DNA (cytosine-5)-methyltransferase, M.Hhal (recognition sequence: GCGC), complexed with S-adenosyl-L-methionine has been determined and refined at 2.5 angstrom resolution. The core of the structure is dominated by sequence motifs conserved among all DNA (cytosine-5)-methyltransferases, and these are responsible for cofactor binding and methyltransferase function.