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

Ravishankar Ramachandran.

SASDJK4 – RNA polymerase core complex

DNA-directed RNA polymerase subunit alpha
DNA-directed RNA polymerase subunit beta
DNA-directed RNA polymerase subunit beta'
DNA-directed RNA polymerase subunit omega
MWexperimental 372 kDa
MWexpected 366 kDa
VPorod 262 nm3
log I(s) 4.59×101 4.59×100 4.59×10-1 4.59×10-2
DNA-directed RNA polymerase subunit alpha DNA-directed RNA polymerase subunit beta DNA-directed RNA polymerase subunit beta' DNA-directed RNA polymerase subunit omega small angle scattering data  s, nm-1
ln I(s)
DNA-directed RNA polymerase subunit alpha DNA-directed RNA polymerase subunit beta DNA-directed RNA polymerase subunit beta' DNA-directed RNA polymerase subunit omega Guinier plot ln 4.60×101 Rg: 5.1 nm 0 (5.1 nm)-2 s2
(sRg)2I(s)/I(0)
DNA-directed RNA polymerase subunit alpha DNA-directed RNA polymerase subunit beta DNA-directed RNA polymerase subunit beta' DNA-directed RNA polymerase subunit omega Kratky plot 1.104 0 3 sRg
p(r)
DNA-directed RNA polymerase subunit alpha DNA-directed RNA polymerase subunit beta DNA-directed RNA polymerase subunit beta' DNA-directed RNA polymerase subunit omega pair distance distribution function Rg: 5.3 nm 0 Dmax: 19.3 nm

Data validation


Fits and models


log I(s)
 s, nm-1
DNA-directed RNA polymerase subunit alpha DNA-directed RNA polymerase subunit beta DNA-directed RNA polymerase subunit beta' DNA-directed RNA polymerase subunit omega DAMFILT model
DNA-directed RNA polymerase subunit alpha DNA-directed RNA polymerase subunit beta DNA-directed RNA polymerase subunit beta' DNA-directed RNA polymerase subunit omega DAMMIF model

Synchrotron SAXS data from solutions of the RNA polymerase core complex in 10 mM Tris-Cl, 100 mM NaCl, 10 mM MgCl2, 0.1 mM EDTA, 5% Glycerol, 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 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 6.40 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.

Sample is likely aggregated.

DNA-directed RNA polymerase subunit alpha (rpoA)
Mol. type   Protein
Organism   Mycobacterium tuberculosis
Olig. state   Dimer
Mon. MW   38.9 kDa
 
UniProt   P9WGZ1 (1-347)
Sequence   FASTA
 
DNA-directed RNA polymerase subunit beta
Mol. type   Protein
Organism   Mycobacterium tuberculosis
Olig. state   Monomer
Mon. MW   129.2 kDa
 
UniProt   P9WGY9 (7-1178)
Sequence   FASTA
 
DNA-directed RNA polymerase subunit beta'
Mol. type   Protein
Organism   Mycobacterium tuberculosis
Olig. state   Monomer
Mon. MW   146.7 kDa
 
UniProt   P9WGY7 (2-1316)
Sequence   FASTA
 
DNA-directed RNA polymerase subunit omega
Mol. type   Protein
Organism   Mycobacterium tuberculosis
Olig. state   Monomer
Mon. MW   11.8 kDa
 
UniProt   P9WGY5 (2-110)
Sequence   FASTA