Strand Passage Mechanism of Type II Topoisomerases
Type IIA topoisomerase operates through a "two-gate" mechanism (though this is a historical notation), a mechanism supported by biochemistry (Roca and Wang) as well as by structural work (Berger and Wang) (see above).
A strand of DNA, called the gate, or G-segment, is bound by a central DNA-binding gate (DNA-gate). A second strand of DNA, called the transport, or T-segment, is captured by the dimerization of the N-terminal ATPase domain (the ATPase-gate) when two molecules of ATP bind. Hydrolysis of ATP and release of an inorganic phosphate leads to the cleavage of the G-segment, as the catalytic tyrosines form a covalent phosphotyrosine bond with the 5' end of the DNA. This creates a four-base overhang and a double-stranded break in the G-segment. As the DNA-binding gate separates, the T-segment is transferred through the G-segment. The G-segment is sealed, leading to the C-terminal gate (or C-gate) to open, allowing for the release of the T-segment. Release of product ADP leads to a reset of the system, and allows a second T-segment to be captured.
Type IIB topoisomerases operate through a similar fashion, except that the protein forms a two-base overhang in the G-segment and the C-terminal gate is completely missing.
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