Fig. 1: Structures of TDP1 and its catalytic site. | Communications Chemistry

Fig. 1: Structures of TDP1 and its catalytic site.

From: Targeted sulfur(VI) fluoride exchange-mediated covalent modification of a tyrosine residue in the catalytic pocket of tyrosyl-DNA phosphodiesterase 1

Fig. 1

a Schematic illustration of phosphodiester substrate and TDP1 catalytic site HKN motifs (black) and residues Y204 and F259 (cyan). b Crystal structure of TDP1(Δ1-148) bound with the vanadate (red spheres) complex of a TOP1-derived peptide (magenta sticks) and DNA substrate (blue sticks) with HKN motifs and Y204 and F259 highlighted (green sticks) (PDB code: 1NOP). c TDP1 tri-complex substrate mimetic with vanadate (red spheres), TOP-derived peptide (magenta sticks) and single-strand DNA substrate (blue sticks) and the catalytic HKN motifs of TDP1 (green sticks) (PDB code: 1NOP). d Crystal structure of TDP1(Δ1-148) complexed with double-stranded DNA (dsDNA) (blue strands) (PDB code: 5NWA). Y204 and F259 are depicted as green sticks. The position of the transition state mimetic vanadate (red spheres) is modeled based on superposition from the coordinates (PDB code: 1NOP).

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