Book of Abstracts: Albany 2007
June 19-23 2007
Structural Basis for 3-Methyladenine Recognition and Removal by a Highly-specific DNA Glycosylase: The Crystal Structure of TAG in Complex with DNA
DNA glycosylases help maintain the genome by excising chemically modified bases from DNA. In bacteria, DNA glycosylases that remove alkylated nucleobases have varying substrate specificities despite their structural similarity. Escherichia coli 3-methyladenine DNA glycosylase I (TAG) specifically catalyzes the removal of the cytotoxic lesion 3-methyladenine (3mA), whereas 3-methyladenine DNA glycosylase II (AlkA) excises a chemically diverse set of alkylated bases. The molecular basis for enzymatic recognition and removal of cationic nucleobases from DNA is currently a matter of speculation, in part due to the lack of a structure of a 3mA-specific glycosylase bound to damaged DNA. Presented here are high-resolution crystal structures of Salmonella typhi TAG in the unliganded form and in complex with DNA containing an abasic site and 3mA nucleobase. Despite its structural similarity to the helix-hairpin-helix superfamily of DNA glycosylases, TAG has evolved a modified strategy for engaging damaged DNA. Extensive interactions between a protein hairpin loop and the bases on both DNA strands provide a structural rationale for how TAG detects 3mA lesions within DNA. Surprisingly, the abasic ribose is not fully flipped into the TAG active site as it is in all other glycosylase-DNA product complexes. Rather, the abasic ribose is only partially rotated around the DNA backbone, which adopts two discrete conformations as a result of the lack of specific contacts with the protein. The TAG base binding pocket provides a tight interface for 3mA nucleobase through extensive hydrogen bonding and aromatic stacking interactions. The tight interaction between TAG and 3mA and the large distance (8 Å) between 3mA and the abasic ribose strongly suggests that conformational relaxation must occur in the DNA upon base hydrolysis. Together with mutational studies of TAG enzymatic activity, these data provide a model for the specific recognition and hydrolysis of 3mA from DNA.
1Department of Biological Sciences and Center for Structural Biology