NMR raw data for: DTX3L ubiquitin ligase ubiquitinates single-stranded nucleic acids
Data files
Oct 15, 2024 version files 13.08 MB
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NMR_data.zip
13.07 MB
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README.md
1.60 KB
Abstract
Ubiquitination typically involves covalent linking of ubiquitin (Ub) to a lysine residue on a protein substrate. Recently, new facets of this process have emerged, including Ub modification of non-proteinaceous substrates like ADP-ribose by the DELTEX E3 ligase family. Here we show that the DELTEX family member DTX3L expands this non-proteinaceous substrate repertoire to include single-stranded DNA and RNA. Although the N-terminal region of DTX3L contains single-stranded nucleic acid binding domains and motifs, the minimal catalytically competent fragment comprises the C-terminal RING and DTC domains (RD). DTX3L-RD catalyses ubiquitination of the 3’-end of single-stranded DNA and RNA, as well as double-stranded DNA with a 3’ overhang of two or more nucleotides. This modification is reversibly cleaved by deubiquitinases. NMR and biochemical analyses reveal that the DTC domain binds single-stranded DNA and facilitates the catalysis of Ub transfer from RING-bound E2-conjugated Ub. Our study unveils the direct ubiquitination of nucleic acids by DTX3L, laying the groundwork for understanding its functional implications.
https://doi.org/10.5061/dryad.rn8pk0pmv
Description of the data and file structure
All NMR data were acquired using a Bruker Avance III 600-MHz spectrometer equipped with a cryogenic triple resonance inverse probe. DTX3L-RD samples were prepared at ~100 uM in 20 mM sodium phosphate, (pH 7.0), 100 mM NaCl, 0.02% NaN3, 1 mM TCEP and 5% D2O with 0.00025% TSP. Experiments were carried out at 298 K, and 1H-15N HSQC spectra were recorded with 16 scans using 200 complex points with a sweep width of 36 parts per million (ppm) in the 15N dimension.
Files and variables
File: NMR_data.zip
Description: The zip file contains raw data for DTX3L RD (RD) alone and titration with three different molar ratios of ADPr (RD + ADPr) or single-stranded nucleic acid (RD + DNA). Below is the list of folders containing these data.
RD
RD + ADPr (1;8)
RD + ADPr (1;42)
RD + ADPr (1;116)
RD + DNA (1;3.75)
RD + DNA (1;7.92)
RD + DNA (1;11.7)
Within each folder is a subfolder named ‘Pdata’ and within this folder is a folder named ‘1’. To view data in Bruker TopSpin 3.5 or CcpNmr AnalysisAssign load spectra from folder ‘1’.
Code/software
For data processing: this can be done by using Bruker TopSpin 3.5 and CcpNmr AnalysisAssign.
Access information
Data was derived from the following sources:
- All NMR data were acquired using a Bruker Avance III 600-MHz spectrometer equipped with a cryogenic triple resonance inverse probe.