The structure of Escherichia coli DNA topoisomerase III
The structure of Escherichia coli DNA topoisomerase III
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DOI：
10.1016/s0969-2126(00)80027-1
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发表时间：
1999-11-15
期刊：
影响因子：
5.7
通讯作者：
DiGate, R
中科院分区：
文献类型：
--
作者：
Mondragón, A;DiGate, R
背景：DNA拓扑异构酶是改变DNA拓扑结构的酶。IA型拓扑异构酶瞬时切割一条DNA链，以便使另一条或多条链通过断裂。以这种方式，它们可以使负超螺旋DNA松弛，并使DNA分子链化和解链。大肠杆菌DNA拓扑异构酶III的结构信息对于理解这种酶的作用机制以及研究同一亚家族不同成员之间的作用机制差异具有重要意义。coli DNA拓扑异构酶III的分辨率已达到3.0埃。结构显示IA型拓扑异构酶的特征性折叠，其由四个结构域形成，产生环形蛋白。与E. coli DNA拓扑异构酶I，虽然四个结构域的相对排列是显着不同的。一个主要的区别是在拓扑异构酶III中存在17个氨基酸的插入，其从中心孔的侧面突出，并且可能参与连环化和去连环化反应。活性位点由高度保守的氨基酸形成，但结构信息和现有的生物化学和诱变数据仍然不足以将特定的作用分配给它们中的大多数。在蛋白质的一侧存在一个沟，这暗示了一个单链DNA（ssDNA）结合区。coliDNA拓扑异构酶III的结构类似于大肠杆菌。大肠杆菌DNA拓扑异构酶I，除了一个带正电荷的环的存在，可能参与连锁和decatenation。蛋白质一侧的凹槽通向活性位点，并且可能参与DNA结合。该结构有助于更有信心地建立IA型拓扑异构酶亚家族的总体机制，并扩展了理解这些蛋白质的结构基础。
Background: DNA topoisomerases are enzymes that change the topology of DNA. Type IA topoisomerases transiently cleave one DNA strand in order to pass another strand or strands through the break. In this manner, they can relax negatively supercoiled DNA and catenate and decatenate DNA molecules. Structural information on Escherichia coli DNA topoisomerase III is important for understanding the mechanism of this type of enzyme and for studying the mechanistic differences among different members of the same subfamily.Results: The structure of the intact and fully active E. coli DNA topoisomerase III has been solved to 3.0 Angstrom resolution. The structure shows the characteristic fold of the type IA topoisomerases that is formed by four domains, creating a toroidal protein. There is remarkable structural similarity to the 67 kDa N-terminal fragment of E. coli DNA topoisomerase I, although the relative arrangement of the four domains is significantly different. A major difference is the presence of a 17 amino acid insertion in topoisomerase III that protrudes from the side of the central hole and could be involved in the catenation and decatenation reactions. The active site is formed by highly conserved amino acids, but the structural information and existing biochemical and mutagenesis data are still insufficient to assign specific roles to most of them. The presence of a groove in one side of the protein is suggestive of a single-stranded DNA (ssDNA)-binding region.Conclusions: The structure of E. coli DNA topoisomerase III resembles the structure of E. coli DNA topoisomerase I except for the presence of a positively charged loop that may be involved in catenation and decatenation. A groove on the side of the protein leads to the active site and is likely to be involved in DNA binding. The structure helps to establish the overall mechanism for the type IA subfamily of topoisomerases with greater confidence and expands the structural basis for understanding these proteins.