Structural and biochemical characterization of RNA polymerase core and UvrD complex: a key component in transcription coupled DNA repair

Ravishankar Ramachandran.

SASDJN4 – ATP-dependent DNA helicase UvrD-ATP complex

ATP-dependent DNA helicase UvrD1
MWexperimental 91 kDa
MWexpected 85 kDa
VPorod 101 nm3
log I(s) 2.83×104 2.83×103 2.83×102 2.83×101
ATP-dependent DNA helicase UvrD1 small angle scattering data  s, nm-1
ln I(s)
ATP-dependent DNA helicase UvrD1 Guinier plot ln 2.83×104 Rg: 3.5 nm 0 (3.5 nm)-2 s2
(sRg)2I(s)/I(0)
ATP-dependent DNA helicase UvrD1 Kratky plot 1.104 0 √3 sRg
p(r)
ATP-dependent DNA helicase UvrD1 pair distance distribution function Rg: 3.3 nm 0 Dmax: 9.5 nm

Data validation

Fits and models

log I(s)
 s, nm-1
ATP-dependent DNA helicase UvrD1 DAMFILT model
log I(s)
 s, nm-1
ATP-dependent DNA helicase UvrD1 MODELLER model
SAXS data from solutions of ATP-dependent DNA helicase UvrD in 10 mM Tris-Cl, 100 mM NaCl, 10 mM MgCl2, 0.1 mM EDTA, 5% Glycerol, pH 8 were collected using an Anton Paar SAXSpace instrument at the CSIR-Central Drug Research Institute (Lucknow, India) using a Dectris Mythen 2R1K detector at a sample-detector distance of 0.3 m and at a wavelength of λ = 0.154 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). One solute concentration of 6.00 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.

The ab initio model displayed in this entry is a DAMFILT averaged spatial representation and may not necessarily reflect the fit to the data. The Rg determined from the Guinier approximation has an error in excess of 0.5 nm.

ATP-dependent DNA helicase UvrD1
Mol. type   Protein
Organism   Mycobacterium tuberculosis
Olig. state   Monomer
Mon. MW   85.0 kDa
 
UniProt   P9WMQ1 (1-771)
Sequence   FASTA