Evolutionary clues to DNA polymerase III beta clamp structural mechanisms

The prokaryotic DNA polymerase III β homodimeric clamp links the replication complex to DNA during polynucleotide synthesis. This clamp is loaded onto DNA and unloaded by the clamp loader complex, the δ subunit of which by itself can bind to and open the clamp. β Clamps from diverse bacteria were examined using contrast hierarchical alignment and interaction network (CHAIN) analysis, a statistical approach that categorizes and measures the evolutionary constraints imposed on protein sequences by natural selection. Some constraints are subtle inasmuch as they are unique to certain bacteria. Examination of corresponding molecular interactions within structures of the Escherichia coli β dimeric and δ–β complexes reveals that N320, Y323 and R176, which are subject to very strong constraints, form a substructure that may serve as a platform for leveraging and directing δ-induced conformational changes. N320 may play a prominent role, as it is strategically situated between this substructure and regions linked to δ binding and opening of β’s dimeric interface. R176 appears to act as a relay between the δ binding site and the clamp’s central hole. Other residues subject to strong constraints are likewise associated with structurally important features. For example, two pairs of interacting residues, R269/E304 and K74/E300, form salt bridges at the dimeric interface, while the C-terminal residues M362, P363, M364 and R365 appear to play key roles in δ binding. Q149 and K198 appear to sense DNA within the clamp’s central hole while other residues may relay this information to the δ binding site. Mutagenesis experiments designed to explore possible mechanisms are proposed.