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

SASDJN2 – Tyrosyl-DNA phosphodiesterase 1 (TDP1)

Tyrosyl-DNA phosphodiesterase 1

MW^experimental	73	kDa
MW^expected	71	kDa
V^Porod	143	nm³

log I(s) 2.62×10² 2.62×10¹ 2.62×10⁰ 2.62×10^-1

Tyrosyl-DNA phosphodiesterase 1 small angle scattering data

s, nm^-1

Log plot Log-Log plot

ln I(s)

Tyrosyl-DNA phosphodiesterase 1 Guinier plot

ln 2.62×10² R_g: 3.2 nm 0 (3.2 nm)^-2 s²

(sR_g)²I(s)/I(0)

Tyrosyl-DNA phosphodiesterase 1 Kratky plot

1.104 0 √3 sR_g

p(r)	R_g: 3.2 nm 0 D_max: 11.7 nm

Data validation

Fits and models

log I(s)	s, nm^-1
+3 Δ/σ -3	s, nm^-1

Tyrosyl-DNA phosphodiesterase 1 BILBOMD model

Synchrotron SAXS data from solutions of tyrosyl-DNA phosphodiesterase 1 (TDP1) 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 (TDP1)
Mol. type		Protein
Organism		Homo sapiens
Olig. state		Monomer
Mon. MW		71.2 kDa

UniProt		Q9NUW8 (1-608)
Sequence		FASTA