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

SASDDQ8 – The complex formed between the class II apurinic/apyrimidinic-endonuclease/3'-5' exonuclease III (XthA) bound to the BRCT domain from Mycobacterium tuberculosis DNA ligase

Probable exodeoxyribonuclease III protein XthA
M. tb. LigA BRCT domain
MWexperimental 46 kDa
MWexpected 48 kDa
VPorod 112 nm3
log I(s) 9.85×101 9.85×100 9.85×10-1 9.85×10-2
Probable exodeoxyribonuclease III protein XthA M. tb. LigA BRCT domain small angle scattering data  s, nm-1
ln I(s)
Probable exodeoxyribonuclease III protein XthA M. tb. LigA BRCT domain Guinier plot ln 9.85×101 Rg: 3.7 nm 0 (3.7 nm)-2 s2
(sRg)2I(s)/I(0)
Probable exodeoxyribonuclease III protein XthA M. tb. LigA BRCT domain Kratky plot 1.104 0 √3 sRg
p(r)
Probable exodeoxyribonuclease III protein XthA M. tb. LigA BRCT domain pair distance distribution function Rg: 4.1 nm 0 Dmax: 18.5 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Probable exodeoxyribonuclease III protein XthA M. tb. LigA BRCT domain DAMFILT model
Synchrotron SAXS data from solutions of the complex formed between exodeoxyribonuclease III (XthA) and the BRCT domain from Mycobacterium tuberculosis DNA ligase in 50 mM Tris-HCl 500 mM NaCl 5mM β-mercaptoethanol, pH 8 were collected on the BM29 beam line at the ESRF (Grenoble, France) using a 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 4.60 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.

The ab initio model displayed in this entry represents the spatially aligned, volume and bead-occupancy-corrected (averaged) representation of the protein (DAMFILT). The displayed fit corresponds to an individual model fit to the SAXS data.

Probable exodeoxyribonuclease III protein XthA (MtbXthA)
Mol. type   Protein
Organism   Mycobacterium tuberculosis
Olig. state   Monomer
Mon. MW   32.9 kDa
 
UniProt   A0A0T9L251
Sequence   FASTA
 
M. tb. LigA BRCT domain (BRCT domain)
Mol. type   Protein
Organism   Mycobacterium tuberculosis
Olig. state   Monomer
Mon. MW   10.3 kDa
 
UniProt   P9WNV1 (601-691)
Sequence   FASTA