Salt bridges at the subdomain interfaces of the adenylation domain and active-site residues of Mycobacterium tuberculosis NAD + -dependent DNA ligase A (MtbLigA) are important for the initial steps of nick-sealing activity

Afsar M, Shukla A, Kumar N, Ramachandran R, Acta Crystallographica Section D Structural Biology 77(6) (2021) DOI

SASDEC6 – Adenylation Domain of DNA ligase A with NAD+

DNA ligase A
MWexperimental 38 kDa
MWexpected 38 kDa
VPorod 94 nm3
log I(s) 5.99×105 5.99×104 5.99×103 5.99×102
DNA ligase A small angle scattering data  s, nm-1
ln I(s)
DNA ligase A Guinier plot ln 6.00×105 Rg: 2.4 nm 0 (2.4 nm)-2 s2
(sRg)2I(s)/I(0)
DNA ligase A Kratky plot 1.104 0 √3 sRg
p(r)
DNA ligase A pair distance distribution function Rg: 2.3 nm 0 Dmax: 6.2 nm

Data validation

Fits and models

log I(s)
 s, nm-1
DNA ligase A DAMMIF model
log I(s)
 s, nm-1
DNA ligase A GASBOR model
SAXS data from solutions of the adenylation Domain of DNA ligase A with NAD+, in 50 mM Tris-HCl, 200 mM NaCl, 2mM β-mercaptoethanol, pH 8 were collected on the Anton Paar SAXSpace instrument at the CSIR-Central Drug Research Institute storage ring (Lucknow, India) using a Hybrid Photon Counting (HPC) Mythen2 R 1K detector at a sample-detector distance of 0.3 m and at a wavelength of λ = 0.154 nm (l(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 10.80 mg/ml was measured at 10°C. Three successive 1800 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
Mol. type   Protein
Organism   Mycobacterium tuberculosis
Olig. state   Monomer
Mon. MW   37.5 kDa
 
UniProt   P9WNV1 (2-328)
Sequence   FASTA