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

doi:10.1038/s41467-017-02530-z

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 journal › Article › peer-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 language	English
Article number	24
Number of pages	13
Journal	Nature Communications
Volume	9
Issue number	1
DOIs	https://doi.org/10.1038/s41467-017-02530-z
Publication status	Published - 2 Jan 2018

Keywords / Materials (for Non-textual outputs)

DNA
DNA damage and repair
mass spectometry
X-ray crystallography

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10.1038/s41467-017-02530-zLicence: Creative Commons: Attribution (CC-BY)

RichardsonEtalNC2018StructuralBasisForDNA3′-EndProcessing
Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/ licenses/by/4.0/. © The Author(s) 2017
Final published version, 2.64 MBLicence: Creative Commons: Attribution (CC-BY)

Reconstituting a DNA repair complex
Richardson, J.
1/06/17 → 31/12/17
Project: University Awarded Project Funding
Repair of covalent protein-DNA complexes
Interthal, H.
MRC
1/06/08 → 31/05/13
Project: Research

Structural basis for DNA 3'-end processing by human Tyrosyl-DNA phosphodiesterase 1
Flett, F. (Creator), Interthal, H. (Creator) & Mackay, C. (Creator), Edinburgh DataShare, 1 Nov 2017
DOI: 10.7488/ds/2243
Dataset
Biochemical data associated with the paper "Structural basis of DNA end processing by Tdp1"
Richardson, J. (Creator), Edinburgh DataShare, 24 Oct 2017
DOI: 10.7488/ds/2237
Dataset

Heidrun Interthal
- School of Biological Sciences - Senior Lecturer
Person: Academic: Research Active
Julia Richardson
- School of Biological Sciences - Senior Lecturer, Director of Teaching
Person: Academic: Research Active

Cite this

@article{83530fb5df4c463b8ceb998420eee90d,

title = "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.",

keywords = "DNA, DNA damage and repair, mass spectometry, X-ray crystallography",

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

year = "2018",

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doi = "10.1038/s41467-017-02530-z",

language = "English",

volume = "9",

journal = "Nature Communications",

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AU - Flett, Fiona J

AU - Ruksenaite, Emilija

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AU - Bharati, Shipra

AU - Carloni, Roberta

AU - Morris, Elizabeth R

AU - Mackay, C Logan

AU - Interthal, Heidrun

AU - Richardson, Julia M

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N2 - 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.

AB - 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.

KW - DNA

KW - DNA damage and repair

KW - mass spectometry

KW - X-ray crystallography

U2 - 10.1038/s41467-017-02530-z

DO - 10.1038/s41467-017-02530-z

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JO - Nature Communications

JF - Nature Communications

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

Abstract / Description of output

Keywords / Materials (for Non-textual outputs)

Access to Document

Fingerprint

Projects

Reconstituting a DNA repair complex

Repair of covalent protein-DNA complexes

Datasets

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

Biochemical data associated with the paper "Structural basis of DNA end processing by Tdp1"

Profiles

Heidrun Interthal

Julia Richardson

Cite this