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

Fiona J Flett, Emilija Ruksenaite, Lee A Armstrong, Shipra Bharati, Roberta Carloni, Elizabeth R Morris, C Logan Mackay, Heidrun Interthal, Julia M Richardson

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

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.

Original languageEnglish
Article number24
Number of pages13
JournalNature Communications
Issue number1
Publication statusPublished - 2 Jan 2018

Keywords / Materials (for Non-textual outputs)

  • DNA
  • DNA damage and repair
  • mass spectometry
  • X-ray crystallography


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