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


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.

SUBMITTER: Flett FJ 

PROVIDER: S-EPMC5750209 | biostudies-literature | 2018 Jan

REPOSITORIES: biostudies-literature

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

Flett Fiona J FJ   Ruksenaite Emilija E   Armstrong Lee A LA   Bharati Shipra S   Carloni Roberta R   Morris Elizabeth R ER   Mackay C Logan CL   Interthal Heidrun H   Richardson Julia M JM  

Nature communications 20180102 1


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 cleava  ...[more]

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