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Depositordc.contributorInterthal, Heidrun
Funderdc.contributor.otherBBSRC - Biotechnology and Biological Sciences Research Councilen_UK
Funderdc.contributor.otherMRC - Medical Research Councilen_UK
Funderdc.contributor.otherScottish Governmenten_UK
Data Creatordc.creatorFlett, Fiona J
Data Creatordc.creatorInterthal, Heidrun
Data Creatordc.creatorMackay, Logan
Date Accessioneddc.date.accessioned2017-11-01T15:51:50Z
Date Availabledc.date.available2017-11-01T15:51:50Z
Citationdc.identifier.citationFlett, 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. https://doi.org/10.7488/ds/2243.en
Persistent Identifierdc.identifier.urihttp://hdl.handle.net/10283/2941
Persistent Identifierdc.identifier.urihttps://doi.org/10.7488/ds/2243
Dataset Description (abstract)dc.description.abstractTyrosyl-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.en_UK
Dataset Description (TOC)dc.description.tableofcontentsMost of the data files are mass spectrometry datasets which are organised according to the figure panels in the manuscript that they feed into. ## Zip files ## The .zip files contain .d directories in Bruker format, produced by mass spectrometry equipment; these directories (once unzipped) can be opened using Bruker DataAnalysis, which is commercial software widely used by mass spectrometry research groups. ### Figure 3C + D ### * For control oligo - Filename: "Hei62-3 trunk H263A xlink_RG6_01_3508.d.zip" * For -2 5IdU oligo - Filename: "Hei66-4 trunk H263A xlink_RG7_01_3491.d.zip" * For -3 5IdU oligo - Filename: "Hei77-1 trunk H263A xlink_RG8_01_3495.d.zip" ### Figure 3E ### * For control oligo - Filename: "Hei62A16_000001.d.zip" * For -2 5IdU oligo - Filename: "Hei66A16_000001.d.zip" * For -3 5IdU oligo - Filename: "Hei77A 16_000002.d.zip" ### Figure 3F ### * For -2 5IdU oligo - Filename: "Hei66A16 iso 740 cid 20 V_000002.d.zip" * For -3 5IdU oligo - Filename: "Hei77A 16 iso 740 cid 20V_000001.d.zip" ## Image files ## In addition there are a few image files, again organised by figure panel: ### Figure 3B ### * Upper panel - Filename: "ff161214 Gels 1-2-3-4.png" * Lower panel - Filename: "ff161214 Coomassie.JPG" ### Figure 6B ### * "Figure 6B.png" (image file derived from ff020715.gel) * "ff020715.gel" (Original ImageQuant file, used for quantitation of data)en_UK
Languagedc.language.isoengen_UK
Publisherdc.publisherUniversity of Edinburgh. School of Biological Sciences. Intitute of Cell Biologyen_UK
Relation (Is Referenced By)dc.relation.isreferencedbyPaper under revision for publication in Nature Communications :Structural basis for DNA 3'-end processing by human Tyrosyl-DNA phosphodiesterase 1en_UK
Rightsdc.rightsCreative Commons Attribution 4.0 International Public Licenseen
Subjectdc.subjectmass spectrometryen_UK
Subjectdc.subjectprotein-DNA crosslinkingen_UK
Subjectdc.subjectTdp1en_UK
Subjectdc.subjectDNA repairen_UK
Subject Classificationdc.subject.classificationBiological Sciencesen_UK
Titledc.titleStructural basis for DNA 3'-end processing by human Tyrosyl-DNA phosphodiesterase 1en_UK
Typedc.typedataseten_UK

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