Escherichia coli 3-methyladenine DNA glycosylase 11 (AlkA) is a DNA repair enzyme that removes numerous alkylated bases from DNA. The three-dimensional structure, mutagenesis and model building studies suggest that the active site is located in a cleft between the two helical domains and that the enzyme flips the target base out of the DNA duplex into the active-site cleft. The structural similarity among a variety of DNA glycosylases shows the existence of a DNA glycosylase superfamily, which includes DNA glycosylases with diverse specificities. Some members are monofunctional and the others have DNA glycosylase/AP-Iyase activities. The replacement of Trp218 by Lys results in enzymes that have AP-Iyase activity but no methylated bases-specific DNA glycosylase activity. The appearance of the altered activity between the wild-type and mutant proteins suggests that the active-site structure of AlkA is much tolerant of different enzyme activities.