M. tuberculosis class II apurinic/ apyrimidinic-endonuclease/3'-5' exonuclease (XthA) engages with NAD+-dependent DNA ligase A (LigA) to counter futile cleavage and ligation cycles in base excision repair.

Khanam T, Afsar M, Shukla A, Alam F, Kumar S, Soyar H, Dolma K, Pasupuleti M, Srivastava KK, Ampapathi RS, Ramachandran R, Nucleic Acids Res (2020) Europe PMC

SASDEX3 – DNA ligase A (MtbLigA) complexed with exodeoxyribonuclease III protein (MtbXthA) in presence of nicked ds DNA

DNA ligase A
Probable exodeoxyribonuclease III protein XthA
Nicked DNA
MWexperimental 136 kDa
MWexpected 117 kDa
VPorod 117 nm3
log I(s) 8.15×100 8.15×10-1 8.15×10-2 8.15×10-3
DNA ligase A Probable exodeoxyribonuclease III protein XthA Nicked DNA small angle scattering data  s, nm-1
ln I(s)
DNA ligase A Probable exodeoxyribonuclease III protein XthA Nicked DNA Guinier plot ln 8.15×100 Rg: 4.5 nm 0 (4.5 nm)-2 s2
(sRg)2I(s)/I(0)
DNA ligase A Probable exodeoxyribonuclease III protein XthA Nicked DNA Kratky plot 1.104 0 3 sRg
p(r)
DNA ligase A Probable exodeoxyribonuclease III protein XthA Nicked DNA pair distance distribution function Rg: 4.8 nm 0 Dmax: 17.1 nm

Data validation


Fits and models


log I(s)
 s, nm-1
DNA ligase A Probable exodeoxyribonuclease III protein XthA Nicked DNA DAMFILT model
DNA ligase A Probable exodeoxyribonuclease III protein XthA Nicked DNA DAMMIF model

Synchrotron SAXS data from solutions of DNA ligase A (MtbLigA) complexed with exodeoxyribonuclease III protein (MtbXthA) in presence of nicked ds DNA in 50 mM Tris-HCl 200 mM NaCl 2mM β-mercaptoethanol (BME), pH 8 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a Dectris Pilatus 1M detector at a sample-detector distance of 1.1 m and at a wavelength of λ = 0.081 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 2.00 mg/ml was measured at 10°C. 10 successive 1 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 A (MtbLigA)
Mol. type   Protein
Organism   Mycobacterium tuberculosis
Olig. state   Monomer
Mon. MW   76.1 kDa
 
UniProt   P9WNV1
Sequence   FASTA
 
Probable exodeoxyribonuclease III protein XthA (MtbXthA)
Mol. type   Protein
Organism   Mycobacterium tuberculosis
Olig. state   Monomer
Mon. MW   32.9 kDa
 
UniProt   A0A0T9L251 (1-291)
Sequence   FASTA
 
Nicked DNA
Mol. type   DNA
Olig. state   Monomer
Mon. MW   8.1 kDa
Sequence   FASTA