3-Methyladenine DNA glycosylase II (AlkA) is a DNA-repair enzyme that removes 
alkylated bases in DNA via the base-excision repair (BER) pathway. The enzyme 
belongs to the helix-hairpin-helix (HhH) superfamily of DNA glycosylases and 
possesses broad substrate specificity. In the genome of Deinococcus radiodurans, 
two genes encoding putative AlkA have been identified (Dr_2074 and Dr_2584). 
Dr_2074 is a homologue of human AlkA (MPG or AAG) and Dr_2584 is a homologue of 
bacterial AlkAs. Here, the three-dimensional structure of Dr_2584 (DrAlkA2) is 
presented and compared with the previously determined structure of Escherichia 
coli AlkA (EcAlkA). The results show that the enzyme consists of two 
helical-bundle domains separated by a wide DNA-binding cleft and contains an HhH 
motif. Overall, the protein fold is similar to the two helical-bundle domains of 
EcAlkA, while the third N-terminal mixed α/β domain observed in EcAlkA is 
absent. Substrate-specificity analyses show that DrAlkA2, like EcAlkA, is able 
to remove both 3-methyladenine (3meA) and 7-methylguanine (7meG) from DNA; 
however, the enzyme possesses no activity towards 1,N(6)-ethenoadenine (ℇA) and 
hypoxanthine (Hx). In addition, it shows activity towards the AlkB dioxygenase 
substrates 3-methylcytosine (3meC) and 1-methyladenine (1meA). Thus, the enzyme 
seems to preferentially repair methylated bases with weakened N-glycosidic 
bonds; this is an unusual specificity for a bacterial AlkA protein and is 
probably dictated by a combination of the wide DNA-binding cleft and a highly 
accessible specificity pocket.