Crystal structure of human thymine DNA glycosylase bound to DNA elucidates sequence‐specific mismatch recognition

Abstract

Cytosine methylation at CpG dinucleotides is central to transcriptional regulation and genome stability and is implicated in genetic disease, cancer, and ageing, a prominent mechanism involving 5‐methylcytosine deamination to give mutagenic G•T mispairs. Human thymine DNA glycosylase (hTDG) excises T from G•T mismatches, and removes other damaged bases, and has specificity for lesions paired with guanine and located at CpG sites. The molecular basis of these important catalytic properties has remained unknown. Here, we report a crystal structure of hTDG (catalytic domain) in complex with abasic DNA reveals that it binds as a protein dimer, one subunit at the abasic site and the other at an undamaged (nonspecific) site. The structure also reveals interactions that provide selectivity for guanine versus adenine as the pairing partner of the target base, and interactions that confer sequence specificity, a highly unusual capability for a DNA glycosylase. We find striking and unexpected differences between hTDG and its prokaryotic ortholog, mismatch‐specific uracil DNA glycosylase (MUG), despite high (32%) sequence identity. This work was supported by a grant from the National Institutes of Health and University of Maryland Greenebaum Cancer Center.