title: A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal domain imparts unidirectional supercoiling bias.
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.
authors.affiliation: Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
authors.forename: Alexander J
authors.initials: AJ
authors.lastname: Ruthenburg
authors.forename: Daina M
authors.initials: DM
authors.lastname: Graybosch
authors.forename: John C
authors.initials: JC
authors.lastname: Huetsch
authors.forename: Gregory L
authors.initials: GL
authors.lastname: Verdine
mesh_terms: D025065:Borrelia burgdorferi / Q000378:metabolism; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry; D027081:DNA Gyrase / Q000737:chemistry* / Q000235:genetics; D027101:DNA Topoisomerase IV / Q000737:chemistry; D004278:DNA, Superhelical; D004583:Electrons; D004926:Escherichia coli / Q000201:enzymology* / Q000235:genetics*; D001411:Geobacillus stearothermophilus / Q000378:metabolism; D008958:Models, Molecular; D010957:Plasmids / Q000378:metabolism; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D055672:Static Electricity; D014616:Vaccinia virus / Q000201:enzymology
chemical_list: D004278:DNA, Superhelical; D004247:DNA; D027101:DNA Topoisomerase IV; D027081:DNA Gyrase