Direct interaction of DNA repair protein tyrosyl DNA phosphodiesterase 1 and the DNA ligase III catalytic domain is regulated by phosphorylation of its flexible N-terminus.

Rashid I, Hammel M, Sverzhinsky A, Tsai MS, Pascal JM, Tainer JA, Tomkinson AE
J Biol Chem :100921 (2021 Jun 25)
PMID: 34181949
doi: 10.1016/j.jbc.2021.100921
Submitted to SASBDB: 2020 Apr 17
Published in SASBDB:

SASDJN2 – Tyrosyl-DNA phosphodiesterase 1 (TDP1)

Tyrosyl-DNA phosphodiesterase 1 experimental SAS data
BILBOMD model
Sample: Tyrosyl-DNA phosphodiesterase 1 monomer, 71 kDa Homo sapiens protein
Buffer: 200 mM NaCl, 20 mM Tris-HCl, pH 7.5, 2% glycerol,, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Jun 26
RgGuinier 3.2 nm
Dmax 11.7 nm
VolumePorod 143 nm3

SASDJQ2 – Dephosphorylated tyrosyl-DNA phosphodiesterase 1 (TDP1-Ppi)

Tyrosyl-DNA phosphodiesterase 1 (dephosphorylated) experimental SAS data
BILBOMD model
Sample: Tyrosyl-DNA phosphodiesterase 1 (dephosphorylated) monomer, 71 kDa Homo sapiens protein
Buffer: 200 mM NaCl, 20 mM Tris-HCl, pH 7.5, 2% glycerol, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Jun 26
RgGuinier 3.2 nm
Dmax 16.5 nm
VolumePorod 141 nm3

SASDJP2 – Truncated tyrosyl-DNA phosphodiesterase 1 (TDP1 149-608)

Tyrosyl-DNA phosphodiesterase 1 (149-608) experimental SAS data
PDB model
Sample: Tyrosyl-DNA phosphodiesterase 1 (149-608) monomer, 53 kDa Homo sapiens protein
Buffer: 200 mM NaCl, 20 mM Tris-HCl, pH 7.5, 2% glycerol,, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Sep 18
RgGuinier 2.3 nm
Dmax 7.0 nm
VolumePorod 80 nm3

SASDJS2 – Truncated DNA ligase 3 bound to tyrosyl-DNA phosphodiesterase 1 (LigIII╬▒(170-755)/TDP1 complex)

Tyrosyl-DNA phosphodiesterase 1Isoform 3 of DNA ligase 3 (DNA ligase III alpha) experimental SAS data
BILBOMD model
Sample: Tyrosyl-DNA phosphodiesterase 1 monomer, 71 kDa Homo sapiens protein
Isoform 3 of DNA ligase 3 (DNA ligase III alpha) monomer, 68 kDa Homo sapiens protein
Buffer: 200 mM NaCl, 40 mM HEPES, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Jul 5
RgGuinier 4.5 nm
Dmax 18.0 nm
VolumePorod 211 nm3

SASDJR2 – DNA ligase 3 bound to tyrosyl-DNA phosphodiesterase 1 (LigIII╬▒/TDP1 complex)

DNA ligase 3 (DNA ligase III alpha)Tyrosyl-DNA phosphodiesterase 1 experimental SAS data
BILBOMD model
Sample: DNA ligase 3 (DNA ligase III alpha), Homo sapiens protein
Tyrosyl-DNA phosphodiesterase 1 monomer, 71 kDa Homo sapiens protein
Buffer: 200 mM NaCl, 40 mM HEPES, pH: 7.5
Experiment: SAXS data collected at 12.3.1 (SIBYLS), Advanced Light Source (ALS) on 2018 Sep 10
RgGuinier 6.5 nm
Dmax 25.5 nm
VolumePorod 790 nm3