The role of monovalent cations in the ATPase reaction of DNA gyrase

Acta Crystallogr D Biol Crystallogr. 2015 Apr;71(Pt 4):996-1005. doi: 10.1107/S1399004715002916. Epub 2015 Mar 27.


Four new crystal structures of the ATPase domain of the GyrB subunit of Escherichia coli DNA gyrase have been determined. One of these, solved in the presence of K(+), is the highest resolution structure reported so far for this domain and, in conjunction with the three other structures, reveals new insights into the function of this domain. Evidence is provided for the existence of two monovalent cation-binding sites: site 1, which preferentially binds a K(+) ion that interacts directly with the α-phosphate of ATP, and site 2, which preferentially binds an Na(+) ion and the functional significance of which is not clear. The crystallographic data are corroborated by ATPase data, and the structures are compared with those of homologues to investigate the broader conservation of these sites.

Keywords: ATPase activity; ATPase domain; DNA gyrase; GHKL superfamily; monovalent cations.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adenosine Triphosphatases / chemistry*
  • Adenosine Triphosphatases / metabolism
  • Adenosine Triphosphate / metabolism
  • Binding Sites
  • Cations, Monovalent / metabolism
  • Crystallography, X-Ray
  • DNA Gyrase / chemistry*
  • DNA Gyrase / metabolism
  • Escherichia coli / chemistry
  • Escherichia coli / enzymology*
  • Escherichia coli / metabolism
  • Models, Molecular
  • Potassium / metabolism
  • Protein Conformation
  • Sodium / metabolism


  • Cations, Monovalent
  • Adenosine Triphosphate
  • Sodium
  • Adenosine Triphosphatases
  • DNA Gyrase
  • Potassium

Associated data

  • PDB/4WUB
  • PDB/4WUC
  • PDB/4WUD
  • PDB/4XTJ