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

SASDEU5 – Adenylation domain of DNA ligase A

DNA ligase A
MWexperimental 37 kDa
MWexpected 38 kDa
VPorod 69 nm3
log I(s) 4.28×104 4.28×103 4.28×102 4.28×101
DNA ligase A small angle scattering data  s, nm-1
ln I(s)
DNA ligase A Guinier plot ln 4.28×104 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: 2.6 nm 0 Dmax: 8.8 nm

Data validation

Fits and models

log I(s)
 s, nm-1
DNA ligase A DAMFILT model
DNA ligase A DAMMIF model
log I(s)
 s, nm-1
DNA ligase A CHIMERA model
SAXS data from solutions of the adenylation domain of DNA ligase A in 50 mM Tris-HCl 200 mM NaCl 2mM β-mercaptoethanol, pH 8 were collected on an Anton Paar SAXSpace instrument at the CSIR-Central Drug Research Institute (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 12.50 mg/ml was measured at 10°C. Two 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.

Ab initio dummy-atom models. Top = averaged spatial representation after multiple modelling runs (DAMFILT); Bottom = an example of an individual ab initio DAM model.

DNA ligase A (AdD)
Mol. type   Protein
Organism   Mycobacterium tuberculosis
Olig. state   Monomer
Mon. MW   37.5 kDa
 
UniProt   P9WNV1 (2-328)
Sequence   FASTA