Short-range translocation by a restriction enzyme motor triggers diffusion along DNA
Short-range translocation by a restriction enzyme motor triggers diffusion along DNA
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DOI：
10.1038/s41589-023-01504-1
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发表时间：
2024-01-02
影响因子：
14.8
通讯作者：
Szczelkun，Mark D.
中科院分区：
文献类型：
--
作者：
Goese，Martin;Magill，Emma E.;Szczelkun，Mark D.
III型限制性修饰酶对噬菌体DNA的切割需要DNA位点之间的长程相互作用。这通过由超家族2解旋酶样ATP酶催化的ATP水解引发的一维扩散（“DNA滑动”）来促进。在这里，我们将基于等离子体DNA折纸纳米转子的超快扭曲测量与停流荧光和基于凝胶的测定相结合，以研究ATP水解的作用。我们的数据表明，解旋酶样结构域具有多种作用。首先，该结构域稳定甲基转移酶亚基旁边的初始DNA相互作用。第二，在第一个ATP水解后，它引起翻转的腺嘌呤碱基的环境变化。最后，它重塑核蛋白的相互作用，通过限制易位的一个105至22-bp的双链DNA环。启动DNA滑动需要马达下游8-15 bp的DNA，对应于核酸酶结构域结合的位点。我们的数据统一了III型酶以前相互矛盾的通信模型。
Cleavage of bacteriophage DNA by the Type III restriction-modification enzymes requires long-range interaction between DNA sites. This is facilitated by one-dimensional diffusion (‘DNA sliding’) initiated by ATP hydrolysis catalyzed by a superfamily 2 helicase-like ATPase. Here we combined ultrafast twist measurements based on plasmonic DNA origami nano-rotors with stopped-flow fluorescence and gel-based assays to examine the role(s) of ATP hydrolysis. Our data show that the helicase-like domain has multiple roles. First, this domain stabilizes initial DNA interactions alongside the methyltransferase subunits. Second, it causes environmental changes in the flipped adenine base following hydrolysis of the first ATP. Finally, it remodels nucleoprotein interactions via constrained translocation of a ∼ 5 to 22-bp double stranded DNA loop. Initiation of DNA sliding requires 8–15 bp of DNA downstream of the motor, corresponding to the site of nuclease domain binding. Our data unify previous contradictory communication models for Type III enzymes.