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

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

DNA ligase 3 (DNA ligase III alpha)
Tyrosyl-DNA phosphodiesterase 1
MWexperimental 340 kDa
MWexpected 71 kDa
VPorod 790 nm3
log I(s) 1.03×102 1.03×101 1.03×100 1.03×10-1
DNA ligase 3 (DNA ligase III alpha) Tyrosyl-DNA phosphodiesterase 1 small angle scattering data  s, nm-1
ln I(s)
DNA ligase 3 (DNA ligase III alpha) Tyrosyl-DNA phosphodiesterase 1 Guinier plot ln 1.04×102 Rg: 6.5 nm 0 (6.5 nm)-2 s2
(sRg)2I(s)/I(0)
DNA ligase 3 (DNA ligase III alpha) Tyrosyl-DNA phosphodiesterase 1 Kratky plot 1.104 0 3 sRg
p(r)
DNA ligase 3 (DNA ligase III alpha) Tyrosyl-DNA phosphodiesterase 1 pair distance distribution function Rg: 6.9 nm 0 Dmax: 25.5 nm

Data validation


Fits and models


log I(s)
 s, nm-1
DNA ligase 3 (DNA ligase III alpha) Tyrosyl-DNA phosphodiesterase 1 BILBOMD model
DNA ligase 3 (DNA ligase III alpha) Tyrosyl-DNA phosphodiesterase 1 BILBOMD model

Synchrotron SAXS data from solutions of the LigIIIα/TDP1 complex in 200 mM NaCl, 40 mM HEPES, pH 7.5 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 3 mg/ml was injected at a 0.50 ml/min flow rate onto a Shodex KW-800 series 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.

DNA ligase 3 (DNA ligase III alpha) (LigIIIα)
Mol. type   Protein
Organism   Homo sapiens
Olig. state   Other
Mon. MW   102.7 kDa
 
UniProt   P49916 (88-1009)
Sequence   FASTA
 
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