Structure of the E. Coli Gyrase DNA Binding and Cleavage Core Reveals A Unique Domain

Abstract

DNA topoisomerases are essential enzymes that sustain chromosome supercoiling homeostasis in all forms of life. DNA gyrase, a heterotetrameric type IIA topoisomerase, has the unique ability to introduce negative supercoils into DNA, helping maintain bacterial genomes in a compact, underwound state. Though all gyrase orthologs use a set of homologous domains and a central “two-gate” mechanism for passing one DNA segment through another, they also exhibit critical family-specific differences. For example, the metal- and DNA-binding TOPRIM domain of gyrases found in many gamma- and beta-proteobacteria contains a 170-amino acid insertion of unknown function. We have solved the crystal structure of the E.coli gyrase DNA binding and cleavage core, visualizing this insertion for the first time. Biochemical analyses of a structure-guided deletion mutant lacking this region reveal that it may help coordinate the activities of gyrase's distal ATPase and DNA binding gates.