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Structural basis for DNA 3′-end processing by human tyrosyl-DNA phosphodiesterase 1

DOI: 10.1038/s41467-017-02530-z DOI Help

Authors: Fiona J. Flett (University of Edinburgh) , Emilija Ruksenaite (University of Edinburgh) , Lee A. Armstrong (University of Edinburgh) , Shipra Bharati (University of Edinburgh) , Roberta Carloni (University of Edinburgh) , Elizabeth R. Morris (University of Edinburgh) , C. Logan Mackay (University of Edinburgh) , Heidrun Interthal (University of Edinburgh) , Julia M. Richardson (University of Edinburgh)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Nature Communications , VOL 9

State: Published (Approved)
Published: January 2018
Diamond Proposal Number(s): 13550

Open Access Open Access

Abstract: Tyrosyl-DNA phosphodiesterase (Tdp1) is a DNA 3′-end processing enzyme that repairs topoisomerase 1B-induced DNA damage. We use a new tool combining site-specific DNA–protein cross-linking with mass spectrometry to identify Tdp1 interactions with DNA. A conserved phenylalanine (F259) of Tdp1, required for efficient DNA processing in biochemical assays, cross-links to defined positions in DNA substrates. Crystal structures of Tdp1–DNA complexes capture the DNA repair machinery after 3′-end cleavage; these reveal how Tdp1 coordinates the 3′-phosphorylated product of nucleosidase activity and accommodates duplex DNA. A hydrophobic wedge splits the DNA ends, directing the scissile strand through a channel towards the active site. The F259 side-chain stacks against the −3 base pair, delimiting the junction of duplexed and melted DNA, and fixes the scissile strand in the channel. Our results explain why Tdp1 cleavage is non-processive and provide a molecular basis for DNA 3′-end processing by Tdp1.

Journal Keywords: DNA; DNA damage and repair; Mass spectrometry; X-ray crystallography

Diamond Keywords: Enzymes

Subject Areas: Biology and Bio-materials, Chemistry

Instruments: I04-1-Macromolecular Crystallography (fixed wavelength) , I04-Macromolecular Crystallography

Added On: 08/01/2018 09:19


Discipline Tags:

Life Sciences & Biotech Biophysics Health & Wellbeing Non-Communicable Diseases Structural biology Chemistry Biochemistry

Technical Tags:

Diffraction Macromolecular Crystallography (MX)