5NW9

Crystal structure of the complex of Tdp1 with duplex DNA

Summary for 5NW9

• Entry DOI: 10.2210/pdb5nw9/pdb
• Descriptor: Tyrosyl-DNA phosphodiesterase 1, DNA (5'-D(P*TP*GP*CP*GP*CP*AP*GP*TP*A)-3') (3 entities in total)
• Functional Keywords: protein-dna complex, dna repair, nucleosidase, phosphotyrosine diesterase, hydrolase
• Biological source: Homo sapiens (Human); More
• Total number of polymer chains: 3
• Total formula weight: 112218.21

Authors

Richardson, J.M.,Ruksenaite, E.,Morris, E.R. (deposition date: 2017-05-05, release date: 2018-01-10, Last modification date: 2024-01-17)

Primary citation

Flett, F.J.,Ruksenaite, E.,Armstrong, L.A.,Bharati, S.,Carloni, R.,Morris, E.R.,Mackay, C.L.,Interthal, H.,Richardson, J.M.
Structural basis for DNA 3'-end processing by human tyrosyl-DNA phosphodiesterase 1.
Nat Commun, 9:24-24, 2018

PubMed 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.

PubMed: 29295983
DOI: 10.1038/s41467-017-02530-z

Experimental method

X-RAY DIFFRACTION (2.04 Å)