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- Title
Structural basis for DNA 3'-end processing by human tyrosyl-DNA phosphodiesterase.
- Authors
Flett, Fiona J.; Carloni, Roberta; Interthal, Heidrun; Ruksenaite, Emilija; Armstrong, Lee A.; Bharati, Shipra; Morris, Elizabeth R.; Richardson, Julia M.; Mackay, C. Logan
- 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.
- Subjects
PROTEIN-tyrosine phosphatase; DNA; PHENYLALANINE; THIAMIN pyrophosphate; NUCLEOSIDASES
- Publication
Nature Communications, 2018, Vol 9, Issue 1, p1
- ISSN
2041-1723
- Publication type
Article
- DOI
10.1038/s41467-017-02530-z