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topoisomerase_a.jpg

Figure 24-16a

topoisomerase_b.jpg

Figure 24-16b

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Description

X-ray structures of yeast topoisomerase II. (a) Structure of a homodimer of the N-terminal ATPase domain (residues 7 406) in complex with AMPPNP as initially viewed with its 2-fold axis vertical. The protein is displayed in ribbon form with one subunit gray and the other colored in rainbow order from its N-terminus (blue) to its C-terminus (red). The bound AMPPNP molecules are shown in space-filling form with C green, N blue, O red, and P orange. (b) Structure of a homodimer of the DNA breakage/reunion domain (residues 419-1177) in complex with a doubly nicked 34-bp DNA. The structure is initially viewed with its twofold axis vertical. The DNA, which describes a 150° arc, is drawn in space-filling form with C green, N blue, O red, and P orange. The protein is displayed in ribbon form with one subunit gray and the other colored in rainbow order from its N-terminus (blue) to its C-terminus (red). The side chains of the two active site Tyr residues (Y782) are shown in space-filling form with C magenta and O red. Note that the Y782 side chain O atoms are positioned to link to opposite DNA strands at sites separated by 4 base pairs. The polypeptides in Parts a and b, which in the intact protein are joined by an 11-reside linker, presumably share the same molecular twofold axis, although their relative orientation about this axis is unknown. [Based on X-ray structures by James Berger, University of California at Berkeley. PDBids 1PVC and 2RGR.]