DNA Polymerase I, Bacterial

DNA polymerase I of eubacteria functions in vivo to synthesize short stretches of DNA during excision repair and to remove RNA primers and fill the gaps between Okazaki fragments in lagging strand replication. Escherichia coli DNA polymerase I, the first DNA polymerase to be discovered and also the first to be studied structurally, serves as an important prototype for this family of enzymes. The bacterial DNA polymerase I enzymes are multifunctional, with three distinct enzymatic activities located on three separate structural domains. In addition to the polymerase activity, there is a 3′–5′ exonuclease that serves to proofread polymerase errors, and a structure-specific 5′ nuclease capable of removing a DNA strand ahead of the site of polymerase addition during synthesis on double-stranded DNA. All three enzymatic activities involve phosphoryl transfer reactions and are dependent on divalent metal ions, bound via carboxylate ligands at each active site. Extensive kinetic studies, together with co-crystal structures of DNA polymerases with bound substrates, have contributed to our understanding of the polymerase reaction pathway. The chemical step of nucleotide addition is preceded by several conformational transitions which contribute to the exquisite specificity and low error rate of DNA polymerases.