Near-atomic structural model for bacterial DNA replication initiation complex and its functional insights
Near-atomic structural model for bacterial DNA replication initiation complex and its functional insights
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DOI：
10.1073/pnas.1609649113
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发表时间：
2016-12-13
影响因子：
11.1
通讯作者：
Takada, Shoji
中科院分区：
文献类型：
--
作者：
Shimizu, Masahiro;Noguchi, Yasunori;Takada, Shoji
在大肠杆菌中，当DNA复制启动时，启动蛋白DNA与染色体起源蛋白oriC和DNA弯曲蛋白IHF形成高阶复合物。虽然DnaA和IHF的三级结构已经被阐明，oriC-DnaA-IHF配合物的动态结构仍然未知。在这里，将计算机模拟与生化分析相结合，我们获得了oric - dna - ihf复合物中心部分的几乎原子分辨率的模型。该复合体可分为三个亚复合体；左亚复合物和右亚复合物包括以头尾方式结合的五聚体dna，中间亚复合物仅包含单个dna。在左亚复合物和右亚复合物中，与各种细胞活性（AAA+）结构域III相关的DNA atp酶在结构域间形成具有特定结构差异的螺旋，从而引起结合DNA的弯曲。在左侧亚复合物中存在一个连续的DNA链，包括IHF插入到DNA环中，与该复合物的DNA解绕功能一致。这些亚复合物的间隙对DNA解绕和DNA解旋酶的装载至关重要。综上所述，该模型提供了一个合理的近原子水平的起始复合物结构解，包括dna亚复合物的动态构象和空间排列。
Upon DNA replication initiation in Escherichia coli, the initiator protein DnaA forms higher-order complexes with the chromosomal origin oriC and a DNA-bending protein IHF. Although tertiary structures of DnaA and IHF have previously been elucidated, dynamic structures of oriC-DnaA-IHF complexes remain unknown. Here, combining computer simulations with biochemical assays, we obtained models at almost-atomic resolution for the central part of the oriC-DnaA-IHF complex. This complex can be divided into three subcomplexes; the left and right subcomplexes include pentameric DnaA bound in a head-to-tail manner and the middle subcomplex contains only a single DnaA. In the left and right subcomplexes, DnaA ATPases associated with various cellular activities (AAA+) domain III formed helices with specific structural differences in interdomain orientations, provoking a bend in the bound DNA. In the left subcomplex a continuous DnaA chain exists, including insertion of IHF into the DNA looping, consistent with the DNA unwinding function of the complex. The intervening spaces in those subcomplexes are crucial for DNA unwinding and loading of DnaB helicases. Taken together, this model provides a reasonable near-atomic level structural solution of the initiation complex, including the dynamic conformations and spatial arrangements of DnaA subcomplexes.