Unlocking and opening a DNA gate

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Abstract
The DNA topoisomerases are enzymes that solve various entanglement problems of intracellular DNA. In their presence, DNA strands or double helices can pass through one another as if there were no physical boundaries in between. Manipulations of DNA by a DNA topoisomerase often require displacements between different parts of the enzyme–DNA complex, over distances of tens of angstroms. Such a requirement is particularly evident in reactions catalyzed by the type II DNA topoisomerases. A type II DNA topoisomerase catalyzes the ATP-dependent transport of one DNA double helix through another (1, 2). Each enzyme is made of two identical halves and possesses two protein gates, an ATP-operated entrance gate that admits the DNA segment to be transported (the T segment), and a second gate for the exit of the admitted T segment after its passage through an enzyme-bound DNA segment termed the G segment (reviewed in refs. 3 and 4; see figure 4B in ref. 4 for a sketch of the type II DNA topoisomerase catalyzed reaction). Slicing a DNA double helix through the entire interface between the two enzyme halves and the enzyme-bound DNA double helix clearly requires large movements within the enzyme–DNA complex. However, there have been few direct studies of such movements before the elegant experiments described in this issue of PNAS by Smiley et al. (5), in which single-molecule fluorescence resonance energy transfer (FRET) is used to monitor the opening and closing of the DNA gate by Drosophila DNA topoisomerase II. Opening a DNA gate by a type II DNA topoisomerase involves unlocking the gate by covalent catalysis that transiently breaks the G segment and widening the gate by moving the two G segment halves away from each other. The unlocking reaction utilizes transesterification chemistry, in which a pair of symmetry-related enzyme tyrosyl groups attack … *E-mail: jcwang{at}fas.harvard.edu