Structural basis for proofreading during replication of the Escherichia coli chromosome
The ϵ subunit of the Escherichia coli replicative DNA polymerase III is the proofreading 3′–5′ exonuclease. Structures of its catalytic N-terminal domain (ϵ186) were determined at two pH values (5.8 and 8.5) at resolutions of 1.7–1.8 Å, in complex with two Mn(II) ions and a nucleotide product of its reaction, thymidine 5′-monophosphate. The protein structure is built around a core five-stranded β sheet that is a common feature of members of the DnaQ superfamily. The structures were identical, except for differences in the way TMP and water molecules are coordinated to the binuclear metal center in the active site. These data are used to develop a mechanism for ϵ and to produce a plausible model of the complex of ϵ186 with DNA.