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

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

Tyrosyl-DNA phosphodiesterase 1 (149-608)
MWexperimental 40 kDa
MWexpected 53 kDa
VPorod 80 nm3
log I(s) 9.50×100 9.50×10-1 9.50×10-2 9.50×10-3
Tyrosyl-DNA phosphodiesterase 1 (149-608) small angle scattering data  s, nm-1
ln I(s)
Tyrosyl-DNA phosphodiesterase 1 (149-608) Guinier plot ln 9.50×100 Rg: 2.3 nm 0 (2.3 nm)-2 s2
(sRg)2I(s)/I(0)
Tyrosyl-DNA phosphodiesterase 1 (149-608) Kratky plot 1.104 0 3 sRg
p(r)
Tyrosyl-DNA phosphodiesterase 1 (149-608) pair distance distribution function Rg: 2.3 nm 0 Dmax: 7.0 nm

Data validation


Fits and models


log I(s)
 s, nm-1
Tyrosyl-DNA phosphodiesterase 1 (149-608) PDB model

Synchrotron SAXS data from solutions of truncated tyrosyl-DNA phosphodiesterase 1 (TDP1 149-608) 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 2 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 (149-608) (TDP1 149-608)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Monomer
Mon. MW   52.9 kDa
 
UniProt   Q9NUW8 (149-698)
Sequence   FASTA
 
PDB code   1JY1