Tyrosyl-DNA phosphodiesterase 1 initiates repair of apurinic/apyrimidinic sites

► We examine an AP site cleavage activity of human Tdp1 in different DNA structures. ► Tdp1 is most active in the cleavage of AP site inside bubble-DNA structure. ► Tdp1 initiates repair of AP site opposite a bulky lesion. ► Tdp1 mutants SCAN1 and H263A fail to cleave AP site.