title: DNA-induced narrowing of the gyrase N-gate coordinates T-segment capture and strand passage.
abstract: DNA gyrase introduces negative supercoils into DNA in an ATP-dependent reaction. DNA supercoiling is catalyzed by a strand-passage mechanism, in which a T-segment of DNA is passed through the gap in a transiently cleaved G-segment. Strand passage requires the coordinated closing and opening of three protein interfaces in gyrase, the N-gate, DNA-gate, and C-gate. We show here that DNA binding to the DNA-gate of gyrase and wrapping of DNA around the C-terminal domains of GyrA induces a narrowing of the N-gate. This half-closed state prepares capture of a T-segment in the upper cavity of gyrase. Subsequent N-gate closure upon binding of ATP then poises the reaction toward strand passage. The N-gate reopens after ATP hydrolysis, allowing for further catalytic cycles. DNA binding, cleavage, and wrapping and N-gate narrowing are intimately linked events that coordinate conformational changes at the DNA and the N-gate.
authors.affiliation: Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, D-48149 Muenster, Germany.
authors.forename: Airat
authors.initials: A
authors.lastname: Gubaev
authors.forename: Dagmar
authors.initials: D
authors.lastname: Klostermeier
mesh_terms: D000255:Adenosine Triphosphate / Q000378:metabolism; D001412:Bacillus subtilis / Q000201:enzymology*; D027081:DNA Gyrase / Q000737:chemistry* / Q000378:metabolism*; D004278:DNA, Superhelical / Q000737:chemistry* / Q000378:metabolism*; D006868:Hydrolysis; D008954:Models, Biological; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011993:Recombinant Fusion Proteins / Q000378:metabolism
chemical_list: D004278:DNA, Superhelical; D011993:Recombinant Fusion Proteins; D000255:Adenosine Triphosphate; D027081:DNA Gyrase