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) Europe PMC

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

Tyrosyl-DNA phosphodiesterase 1 (dephosphorylated)
MWexperimental 64 kDa
MWexpected 71 kDa
VPorod 141 nm3
log I(s) 2.35×102 2.35×101 2.35×100 2.35×10-1
Tyrosyl-DNA phosphodiesterase 1 (dephosphorylated) small angle scattering data  s, nm-1
ln I(s)
Tyrosyl-DNA phosphodiesterase 1 (dephosphorylated) Guinier plot ln 2.36×102 Rg: 3.2 nm 0 (3.2 nm)-2 s2
Tyrosyl-DNA phosphodiesterase 1 (dephosphorylated) Kratky plot 1.104 0 3 sRg
Tyrosyl-DNA phosphodiesterase 1 (dephosphorylated) pair distance distribution function Rg: 3.6 nm 0 Dmax: 16.5 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Tyrosyl-DNA phosphodiesterase 1 (dephosphorylated) BILBOMD model
Tyrosyl-DNA phosphodiesterase 1 (dephosphorylated) BILBOMD model

Synchrotron SAXS data from solutions of dephosphorylated tyrosyl-DNA phosphodiesterase 1 (TDP1-Ppi) in 200 mM NaCl, 20 mM Tris-HCl, pH 7.5, 2% glycerol, were collected on the 12.3.1 (SIBYLS) beam line at the Advanced Light Source (ALS; Berkeley, CA, USA) using a Pilatus3 X 2M detector at a sample-detector distance of 2.1 m and at a wavelength of λ = 0.1127 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 50.00 μl sample at 10 mg/ml was injected at a 0.50 ml/min flow rate onto a Shodex KW402.5-4F column at 20°C. 600 successive 3 second frames were collected. The data were normalized to the intensity of the transmitted beam and radially averaged; the scattering of the solvent-blank was subtracted.

Tyrosyl-DNA phosphodiesterase 1 (dephosphorylated) (TDP1-Ppi)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   71.2 kDa
UniProt   Q9NUW8 (1-608)
Sequence   FASTA