Flexibility revealed by the 1.85 Å crystal structure of the β sliding-clamp subunit of Escherichia coli DNA polymerase III

The β subunit of the Escherichia coli replicative DNA polymerase III holoenzyme is the sliding clamp that interacts with the α (polymerase) subunit to maintain the high processivity of the enzyme. The β protein is a ring-shaped dimer of 40.6 kDa subunits whose structure has previously been determined at a resolution of 2.5 Å [Kong et al. (1992), Cell, 69, 425–437]. Here, the construction of a new plasmid that directs overproduction of β to very high levels and a simple procedure for large-scale purification of the protein are described. Crystals grown under slightly modified conditions diffracted to beyond 1.9 Å at 100 K at a synchrotron source. The structure of the β dimer solved at 1.85 Å resolution shows some differences from that reported previously. In particular, it was possible at this resolution to identify residues that differed in position between the two subunits in the unit cell; side chains of these and some other residues were found to occupy alternate conformations. This suggests that these residues are likely to be relatively mobile in solution. Some implications of this flexibility for the function of β are discussed.