The GyrA-box determines the geometry of DNA bound to gyrase and couples DNA binding to the nucleotide cycle

Abstract

DNA gyrase catalyses the adenosine triphosphate-dependent introduction of negative supercoils into DNA. The enzyme binds a DNA-segment at the so-called DNA-gate and cleaves both DNA strands. DNA extending from the DNA-gate is bound at the perimeter of the cylindrical C-terminal domains (CTDs) of the GyrA subunit. The CTDs are believed to contribute to the wrapping of DNA around gyrase in a positive node as a prerequisite for strand passage towards negative supercoiling. A conserved seven amino acid sequence motif in the CTD, the so-called GyrA-box, has been identified as a hallmark feature of gyrases. Mutations of the GyrA-box abolish supercoiling. We show here that the GyrA-box marginally stabilizes the CTDs. Although it does not contribute to DNA binding, it is required for DNA bending and wrapping, and it determines the geometry of the bound DNA. Mutations of the GyrA-box abrogate a DNA-induced conformational change of the gyrase N-gate and uncouple DNA binding and adenosine triphosphate hydrolysis. Our results implicate the GyrA-box in coordinating DNA binding and the nucleotide cycle. © 2012 The Author(s).