Human thymine DNA glycosylase (hTDG) efficiently excises
5-carboxylcytosine (5caC), a key oxidation product of
5-methylcytosine in genomic DNA, in a recently discovered
cytosine demethylation pathway. We present here the crystal
structures of the hTDG catalytic domain in complex with
duplex DNA containing either 5caC or a fluorinated analog.
These structures, together with biochemical and computational
analyses, reveal that 5caC is specifically recognized in
the active site of hTDG, supporting the role of TDG in mammalian
5-methylcytosine demethylation.