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: 2020 Apr 27

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

R_g^Guinier	3.2	nm
D_max	11.7	nm
Volume^Porod	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

R_g^Guinier	3.2	nm
D_max	16.5	nm
Volume^Porod	141	nm³

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

Tyrosyl-DNA phosphodiesterase 1 (149-608) experimental SAS data

PDB (PROTEIN DATA BANK) 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

R_g^Guinier	2.3	nm
D_max	7.0	nm
Volume^Porod	80	nm³

SASDJS2 – Truncated DNA ligase 3 bound to tyrosyl-DNA phosphodiesterase 1 (LigIIIα(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

R_g^Guinier	4.5	nm
D_max	18.0	nm
Volume^Porod	211	nm³

SASDJR2 – DNA ligase 3 bound to tyrosyl-DNA phosphodiesterase 1 (LigIIIα/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

R_g^Guinier	6.5	nm
D_max	25.5	nm
Volume^Porod	790	nm³