Structure and flexibility of the DNA polymerase holoenzyme of vaccinia virus.

Burmeister WP, Boutin L, Balestra AC, Gröger H, Ballandras-Colas A, Hutin S, Kraft C, Grimm C, Böttcher B, Fischer U, Tarbouriech N, Iseni F, PLoS Pathog 20(5):e1011652 (2024) Europe PMC

SASDSW8 – Apo form of vaccinia virus polymerase holoenzyme E9-A20-D4

DNA polymerase
DNA polymerase processivity factor component OPG148
Uracil-DNA glycosylase
MWexperimental 212 kDa
MWexpected 194 kDa
VPorod 350 nm3
log I(s) 1.25×102 1.25×101 1.25×100 1.25×10-1
DNA polymerase DNA polymerase processivity factor component OPG148 Uracil-DNA glycosylase small angle scattering data  s, nm-1
ln I(s)
DNA polymerase DNA polymerase processivity factor component OPG148 Uracil-DNA glycosylase Guinier plot ln 1.26×102 Rg: 5.0 nm 0 (5.0 nm)-2 s2
(sRg)2I(s)/I(0)
DNA polymerase DNA polymerase processivity factor component OPG148 Uracil-DNA glycosylase Kratky plot 1.104 0 3 sRg
p(r)
DNA polymerase DNA polymerase processivity factor component OPG148 Uracil-DNA glycosylase pair distance distribution function Rg: 5.2 nm 0 Dmax: 18 nm

Data validation


There are no models related to this curve.

Synchrotron SAXS data from solutions of the vaccinia virus polymerase holoenzyme E9-A20-D4 in 200 mM NaCl, 20 mM Tris-HCl and 1 mM TCEP, pH 8.5 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 = 0.099 nm (I(s) vs s, where s = 4πsinθ/λ, and 2θ is the scattering angle). In-line size-exclusion chromatography (SEC) SAS was employed. The SEC parameters were as follows: A 45.00 μl sample at 2 mg/ml was injected at a 0.10 ml/min flow rate onto a GE Superdex 200 Increase 3.2/300 column at 20°C. 2000 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 E9-A20-D4 polymerase holoenzyme with a 1:1:1 stoichiometry.

DNA polymerase (E9)
Mol. type   Protein
Organism   Vaccinia virus (strain Copenhagen)
Olig. state   Monomer
Mon. MW   117.2 kDa
 
UniProt   P20509 (2-1006)
Sequence   FASTA
 
DNA polymerase processivity factor component OPG148 (A20)
Mol. type   Protein
Organism   Vaccinia virus (strain Copenhagen)
Olig. state   Monomer
Mon. MW   49.2 kDa
 
UniProt   P20995 (1-426)
Sequence   FASTA
 
Uracil-DNA glycosylase (D4)
Mol. type   Protein
Organism   Vaccinia virus (strain Copenhagen)
Olig. state   Monomer
Mon. MW   27.5 kDa
 
UniProt   P20536 (1-218)
Sequence   FASTA