Structural and functional analyses of an archaeal XPF/Rad1/Mus81 nuclease: Asymmetric DNA binding and cleavage mechanisms
Structural and functional analyses of an archaeal XPF/Rad1/Mus81 nuclease: Asymmetric DNA binding and cleavage mechanisms
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DOI：
10.1016/j.str.2005.04.024
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发表时间：
2005-08-01
期刊：
影响因子：
5.7
通讯作者：
Morikawa, K
中科院分区：
文献类型：
--
作者：
Nishino, T;Komori, K;Morikawa, K
XPF/Rad1/Mus81/Hef 蛋白识别并切割分支 DNA 结构。 XPF 和 Rad1 蛋白裂解核仁切除修复泡的 51 侧，而 Mus81 和 Hef 裂解切口霍利迪连接、叉或瓣结构的类似位点。这些蛋白质均以二聚体的形式发挥作用，并由催化结构域和螺旋-发夹-螺旋 DNA 结合 (HhH) 结构域组成。我们确定了激烈火球菌 Hef 核酸酶 (HefHhH) 的 HhH 结构域的晶体结构，揭示了蛋白质二聚化的独特模式。我们的结构和生化分析还表明，每个催化结构域和 HhH 结构域都与叉状结构 DNA 内的不同区域结合：来自两个单独亚基的每个 HhH 结构域不对称地与臂区域结合，而催化结构域在连接中心附近结合。与 DNA 结合后，Hef 核酸酶会破坏切割位点附近的碱基对。这种二分结合模式很可能在 XPF/Rad1/Mus81 核酸酶家族中是保守的。
XPF/Rad1/Mus81/Hef proteins recognize and cleave branched DNA structures. XPF and Rad1 proteins cleave the 51 side of nucleoticle excision repair bubble, while Mus81 and Hef cleave similar sites of the nicked Holliday junction, fork, or flap structure. These proteins all function as dimers and consist of catalytic and helix-hairpin-helix DNA binding (HhH) domains. We have determined the crystal structure of the HhH domain of Pyrococcus furiosus Hef nuclease (HefHhH), which revealed the distinct mode of protein dimerization. Our structural and biochemical analyses also showed that each of the catalytic and HhH domains binds to distinct regions within the forkstructured DNA: each HhH domain from two separate subunits asymmetrically binds to the arm region, while the catalytic domain binds near the junction center. Upon binding to DNA, Hef nuclease disrupts base pairs near the cleavage site. It is most likely that this bipartite binding mode is conserved in the XPF/ Rad1/Mus81 nuclease family.