Comparison of gyrase proteins and mechanism of enzyme action. (A) Domains and secondary structures predicted from amino acid sequences of GyrA and GyrB from E. coli, P. falciparum, and T. gondii GT1. Proteins are depicted at constant length regardless of their actual molecular weight. Domains were predicted by Pfam  and secondary structures were predicted by the SOPMA server . (B) Schematic mechanism of supercoiling by DNA gyrase: (i) GyrB and GyrA dimers assemble on a piece of DNA. (ii) A protein-DNA complex is formed when the G-segment (“G”) binds to the active site of the enzyme at the DNA gate (“D”). (iii) The N-terminal regions of GyrB (shown in purple, “N”) dimerize upon ATP binding and capture the T-segment (“T”). The G segment is cleaved across both strands. This cleaved conformation is trapped by gyrase poisons such as the fluoroquinolones (FQ) and is lethal to the cell. (iv) The DNA gate is opened and the T-segment is transported into the lower cavity of the enzyme. (v) The exit gate (“E”) of the enzyme opens and the T-segment passes out. A single cycle of supercoiling is complete while two ATP are hydrolyzed.