Regulation of futile ligation during early steps of BER in M. tuberculosis is carried out by a β-clamp-XthA-LigA tri-component complex

Shukla A, Afsar M, Khanam T, Kumar N, Ali F, Kumar S, Jahan F, Ramachandran R, International Journal of Biological Macromolecules (2022) DOI

SASDFF6 – Probable exodeoxyribonuclease III protein XthA, sliding beta clamp complex

Beta sliding clamp
Probable exodeoxyribonuclease III protein XthA (Exonuclease III) (EXO III) (AP endonuclease VI)
MWexperimental 125 kDa
MWexpected 119 kDa
VPorod 98 nm3
log I(s) 1.29×101 1.29×100 1.29×10-1 1.29×10-2
Beta sliding clamp Probable exodeoxyribonuclease III protein XthA (Exonuclease III) (EXO III) (AP endonuclease VI) small angle scattering data  s, nm-1
ln I(s)
Beta sliding clamp Probable exodeoxyribonuclease III protein XthA (Exonuclease III) (EXO III) (AP endonuclease VI) Guinier plot ln 1.30×101 Rg: 3.5 nm 0 (3.5 nm)-2 s2
(sRg)2I(s)/I(0)
Beta sliding clamp Probable exodeoxyribonuclease III protein XthA (Exonuclease III) (EXO III) (AP endonuclease VI) Kratky plot 1.104 0 √3 sRg
p(r)
Beta sliding clamp Probable exodeoxyribonuclease III protein XthA (Exonuclease III) (EXO III) (AP endonuclease VI) pair distance distribution function Rg: 3.5 nm 0 Dmax: 11.3 nm

Data validation

Fits and models

log I(s)
 s, nm-1
Beta sliding clamp Probable exodeoxyribonuclease III protein XthA (Exonuclease III) (EXO III) (AP endonuclease VI) DAMMIF model
Synchrotron SAXS data from solutions of probable exodeoxyribonuclease III protein XthA bound to sliding beta clamp in 50 mM Tris-HCl, 200 mM NaCl, 2 mM β-mercaptoethanol, pH 8 were collected on the BM29 beam line at the ESRF storage ring (Grenoble, France) using a Pilatus 1M detector at a sample-detector distance of 2.9 m and at a wavelength of λ = 0.0992 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 2.50 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 presented model shows the spatial alignment of several individually calculated models and does not fit the SAXS data. A corresponding individual model fit (individual model not provided for this entry) is shown.

Beta sliding clamp
Mol. type   Protein
Organism   Mycobacterium tuberculosis
Olig. state   Dimer
Mon. MW   42.9 kDa
 
UniProt   P9WNU1 (1-402)
Sequence   FASTA
 
Probable exodeoxyribonuclease III protein XthA (Exonuclease III) (EXO III) (AP endonuclease VI)
Mol. type   Protein
Organism   Mycobacterium tuberculosis
Olig. state   Monomer
Mon. MW   32.9 kDa
 
UniProt   P96273 (1-291)
Sequence   FASTA