Self-association Equilibria of Escherichia coli UvrD Helicase Studied by Analytical Ultracentrifugation

The Escherichia coli UvrD protein (helicase II) is an SF1 superfamily helicase required for methyl-directed mismatch repair and nucleotide excision repair of DNA. We have characterized quantitatively the self-assembly equilibria of the UvrD protein as a function of [NaCl], [glycerol], and temperature (5–35 °C; pH 8.3) using analytical sedimentation velocity and equilibrium techniques, and find that UvrD self-associates into dimeric and tetrameric species over a range of solution conditions (t≤25 °C). Increasing [NaCl] from 20 mM to 200 mM decreases the dimerization equilibrium constant (L20) from 2.33(±0.30) μM−1 to 0.297(±0.006) μM−1 (pH 8.3, 20% (v/v) glycerol, 25 °C). The overall tetramerization equilibrium constant (L40) is 5.11(±0.80) μM−3 at 20 mM NaCl, but decreases so that it is not measurable at 200 mM NaCl. At 500 mM NaCl, only UvrD monomers are detectable. Increasing [glycerol] over the range from 20% to 40% (v/v) decreases both L20 and L40. We find no evidence for hexamer formation, although a species consistent in size with an octamer is detected at 35 °C. Inclusion of either ADP or ATPγS does not affect either L20 or L40 significantly, and does not induce the formation of additional assembly states. We also investigated the stoichiometry of UvrD binding to a 3′-(dT)20-18 bp DNA substrate by sedimentation equilibrium. At saturating concentrations of UvrD, three UvrD monomers can bind to the DNA substrate, although only two UvrD monomers are required to form a processive helicase complex. When the total DNA substrate concentration is about twofold greater than the total UvrD concentration, the vast majority of the DNA is bound by a single UvrD monomer.