A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal domain imparts unidirectional supercoiling bias

J Biol Chem. 2005 Jul 15;280(28):26177-84. doi: 10.1074/jbc.M502838200. Epub 2005 May 15.

Abstract

DNA gyrase is unique among type II topoisomerases in that its DNA supercoiling activity is unidirectional. The C-terminal domain of the gyrase A subunit (GyrA-CTD) is required for this supercoiling bias. We report here the x-ray structure of the Escherichia coli GyrA-CTD (Protein Data Bank code 1ZI0). The E. coli GyrA-CTD adopts a circular-shaped beta-pinwheel fold first seen in the Borrelia burgdorferi GyrA-CTD. However, whereas the B. burgdorferi GyrA-CTD is flat, the E. coli GyrA-CTD is spiral. DNA relaxation assays reveal that the E. coli GyrA-CTD wraps DNA inducing substantial (+) superhelicity, while the B. burgdorferi GyrA-CTD introduces a more modest (+) superhelicity. The observation of a superhelical spiral in the present structure and that of the Bacillus stearothermophilus ParC-CTD structure suggests unexpected similarities in substrate selectivity between gyrase and Topo IV enzymes. We propose a model wherein the right-handed ((+) solenoidal) wrapping of DNA around the E. coli GyrA-CTD enforces unidirectional (-) DNA supercoiling.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Borrelia burgdorferi / metabolism
  • Crystallography, X-Ray
  • DNA / chemistry
  • DNA Gyrase / chemistry*
  • DNA Gyrase / genetics
  • DNA Topoisomerase IV / chemistry
  • DNA, Superhelical*
  • Electrons
  • Escherichia coli / enzymology*
  • Escherichia coli / genetics*
  • Geobacillus stearothermophilus / metabolism
  • Models, Molecular
  • Plasmids / metabolism
  • Protein Conformation
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Static Electricity
  • Vaccinia virus / enzymology

Substances

  • DNA, Superhelical
  • DNA
  • DNA Topoisomerase IV
  • DNA Gyrase

Associated data

  • PDB/1ZI0