Model building of DNA repair enzyme 3-methyladenine DNA glycosylase-DNA complex.

We report the model structure of enzyme-DNA complex based on X-ray structure of 3-methyladenine-DNA glycosylase II and mutagenic studies. The enzyme structure does not have any recognizable DNA binding motifs. The DNA was located in the large cleft between the two all alpha domains with the damaged adenine base moiety (3-methyladenine) of DNA duplex positioned in the entrance region of the cleft including the tryptophan and aspartic acid residues. For the target 3-methyladenine to interact with these residues, the 3-methyladenine has to flipped out from the DNA helix. A number of the positively charged amino acid residues adopt at the negatively charged phosphate moieties. It is necessary to kink the DNA helix slightly to form the good interactions between both molecules. The damaged base must be held in place by a number of interactions including the weak van der Waals and electrostatic attractions.