Structural basis of the nucleotide incorporation cycle of bacterial DNA polymerase III

Abstract

Bacterial DNA polymerase III (PolIII) is the primary replicative polymerase responsible for faithful genome duplication, yet high-resolution structural snapshots of the enzyme during DNA synthesis and proofreading have remained elusive. Here we determine cryo-EM structures of the Escherichia coli PolIII core-clamp-DNA binary, ternary and proofreading complexes at 2.4-2.7 [A] resolution, revealing the structural basis of nucleotide selection, incorporation and proofreading. Binding of an incoming nucleotide expels the single-stranded template overhang from the polymerase central channel and induces a large rotation of the polymerase index finger, which closes around the incoming nucleotide to form a compact nascent base-pair-binding pocket. A conserved tyrosine on the finger stacks against the incoming nucleotide to impose stringent steric constraints that promote nucleotide selection, whereas a conserved histidine acts as a steric gate to exclude ribonucleotides. The proofreading structures capture key intermediates that reveal how PolIII transfers a mismatched primer terminus to the 3'-5' exonuclease active site and excises the misincorporated nucleotide while avoiding unnecessary degradation of correctly paired DNA. Together, these findings define the molecular mechanism by which the bacterial replicative polymerase couples rapid and processive DNA synthesis with exceptional replication fidelity.