Edinburgh Research Explorer

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

Dataset

Related Edinburgh Organisations

PublisherEdinburgh DataShare
Date made available1 Nov 2017

Description

Most of the data files are mass spectrometry datasets which are organised according to the figure panels in the manuscript that they feed into.

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.

Data Citation

Flett, Fiona J; Interthal, Heidrun; Mackay, Logan. (2017). Structural basis for DNA 3'-end processing by human Tyrosyl-DNA phosphodiesterase 1, [dataset]. University of Edinburgh. School of Biological Sciences. Intitute of Cell Biology. http://dx.doi.org/10.7488/ds/2243.

Access status

Open

ID: 46251427