Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
Crit Rev Biochem Mol Biol. 2010 Dec;45(6):520-34. doi: 10.3109/10409238.2010.513375.
The processes of DNA topoisomerization and site-specific recombination are fundamentally similar: DNA cleavage by forming a phospho-protein covalent linkage, DNA topological rearrangement, and DNA ligation coupled with protein regeneration. Type IB DNA topoisomerases are structurally and mechanistically homologous to tyrosine recombinases. Both enzymes nick DNA double helices independent of metal ions, form 3'-phosphotyrosine intermediates, and rearrange the free 5' ends relative to the uncut strands by swiveling. In contrast, serine recombinases generate 5'-phospho-serine intermediates. A 180° relative rotation of the two halves of a 100 kDa terameric serine recombinase and DNA complex has been proposed as the mechanism of strand exchange. Here I propose an alternative mechanism. Interestingly, the catalytic domain of serine recombinases has structural similarity to the TOPRIM domain, conserved among all Type IA and Type II topoisomerases and responsible for metal binding and DNA cleavage. TOPRIM topoisomerases also cleave DNA to generate 5'-phosphate and 3'-OH groups. Based on the existing biochemical data and crystal structures of topoisomerase II and serine recombinases bound to pre- and post-cleavage DNA, I suggest a strand passage mechanism for DNA recombination by serine recombinases. This mechanism is reminiscent of DNA topoisomerization and does not require subunit rotation.
DNA 拓扑异构酶和位点特异性重组的过程在本质上是相似的：通过形成磷酸化蛋白共价键来切割 DNA、DNA 拓扑重排、与蛋白质再生偶联的 DNA 连接。IB 型 DNA 拓扑异构酶在结构和机制上与酪氨酸重组酶同源。这两种酶都不依赖于金属离子切割 DNA 双螺旋，形成 3'-磷酸酪氨酸中间体，并通过旋转使游离的 5' 端相对于未切割链进行拓扑重排。相比之下，丝氨酸重组酶产生 5'-磷酸丝氨酸中间体。已经提出了一种 100 kDa 三聚体丝氨酸重组酶和 DNA 复合物的两半相对旋转 180°的机制，作为链交换的机制。在这里，我提出了一种替代机制。有趣的是，丝氨酸重组酶的催化结构域与 TOPRIM 结构域具有结构相似性，TOPRIM 结构域在所有 IA 型和 II 型拓扑异构酶中保守，负责金属结合和 DNA 切割。TOPRIM 拓扑异构酶也能切割 DNA 生成 5'-磷酸和 3'-OH 基团。基于拓扑异构酶 II 和丝氨酸重组酶与预切割和切割后 DNA 结合的现有生化数据和晶体结构，我提出了一种丝氨酸重组酶介导 DNA 重组的链转移机制。这种机制让人联想到 DNA 拓扑异构化，并且不需要亚基旋转。
