Dong Ken C, Berger James M
Chemical Biology Graduate Program, Department of Chemistry, College of Chemistry, University of California, Berkeley, California 94720-3220, USA.
Nature. 2007 Dec 20;450(7173):1201-5. doi: 10.1038/nature06396.
Type II topoisomerases disentangle DNA to facilitate chromosome segregation, and represent a major class of therapeutic targets. Although these enzymes have been studied extensively, a molecular understanding of DNA binding has been lacking. Here we present the structure of a complex between the DNA-binding and cleavage core of Saccharomyces cerevisiae Topo II (also known as Top2) and a gate-DNA segment. The structure reveals that the enzyme enforces a 150 degrees DNA bend through a mechanism similar to that of remodelling proteins such as integration host factor. Large protein conformational changes accompany DNA deformation, creating a bipartite catalytic site that positions the DNA backbone near a reactive tyrosine and a coordinated magnesium ion. This configuration closely resembles the catalytic site of type IA topoisomerases, reinforcing an evolutionary link between these structurally and functionally distinct enzymes. Binding of DNA facilitates opening of an enzyme dimerization interface, providing visual evidence for a key step in DNA transport.
II型拓扑异构酶解开DNA以促进染色体分离，是一类主要的治疗靶点。尽管这些酶已被广泛研究，但对DNA结合的分子理解一直缺乏。在此，我们展示了酿酒酵母拓扑异构酶II（也称为Top2）的DNA结合和切割核心与一个门控DNA片段之间的复合物结构。该结构表明，该酶通过一种类似于整合宿主因子等重塑蛋白的机制使DNA产生150度的弯曲。DNA变形伴随着蛋白质的大量构象变化，形成了一个二分催化位点，该位点将DNA主链定位在一个反应性酪氨酸和一个配位镁离子附近。这种构型与IA型拓扑异构酶的催化位点非常相似，加强了这些结构和功能不同的酶之间的进化联系。DNA的结合促进了酶二聚化界面的打开，为DNA转运中的关键步骤提供了直观证据。
