Structural basis of the interaction between Topoisomerase IIIβ and the TDRD3 auxiliary factor.
Structural basis of the interaction between Topoisomerase IIIβ and the TDRD3 auxiliary factor.
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DOI：
10.1038/srep42123
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发表时间：
2017-02-08
影响因子：
4.6
通讯作者：
Fukai S
中科院分区：
文献类型：
--
作者：
Goto-Ito S;Yamagata A;Takahashi TS;Sato Y;Fukai S
拓扑异构酶IIIβ（Topoisomerase III β，TOP 3 β）是一种DNA/RNA拓扑异构酶，参与基因表达的表观遗传或翻译调控。在细胞中，TOP 3 β与其特异性辅助因子TDRD 3共存。TDRD 3作为一种支架蛋白，将TOP 3 β募集到其DNA/RNA底物中，在特定的细胞位点积累，如甲基化染色质或神经应激颗粒。本文报道了TOP3β的催化结构域、TDRD 3的DUF 1767-OB折叠结构域及其复合物的晶体结构，分辨率分别为3.44 nm、1.62 nm和3.6 nm。TOP3β的环形催化结构域结合TDRD 3的OB-折叠结构域。TDRD 3 OB-折叠结构域包含插入环，其从核心结构突出。插入环和核心区都与TOP 3 β相互作用。我们的下拉结合试验表明，疏水性的核心表面和插入环的氨基和羧基末端区域的相互作用是必不可少的。通过与拓扑异构酶IIIα（Topoisomerase IIIα，TOP3α）-RMI 1复合物结构的比较，确定Arg 96、Val 109、Phe 139和TDRD 3的短插入环是与TOP3β特异性相互作用的关键结构元件，避免了与TOP3α的非同源相互作用。
Topoisomerase IIIβ (TOP3β) is a DNA/RNA topoisomerase that has been implicated in epigenetic or translational control of gene expression. In cells, TOP3β co-exists with its specific auxiliary factor, TDRD3. TDRD3 serves as a scaffold protein to recruit TOP3β to its DNA/RNA substrates accumulating in specific cellular sites such as methylated chromatins or neural stress granules. Here we report the crystal structures of the catalytic domain of TOP3β, the DUF1767–OB-fold domains of TDRD3 and their complex at 3.44 Å, 1.62 Å and 3.6 Å resolutions, respectively. The toroidal-shaped catalytic domain of TOP3β binds the OB-fold domain of TDRD3. The TDRD3 OB-fold domain harbors the insertion loop, which is protruding from the core structure. Both the insertion loop and core region interact with TOP3β. Our pull-down binding assays showed that hydrophobic characters of the core surface and the amino- and carboxy-terminal regions of the insertion loop are essential for the interaction. Furthermore, by comparison with the structure of the homologous Topoisomerase IIIα (TOP3α)–RMI1 complex, we identified Arg96, Val109, Phe139 and the short insertion loop of TDRD3 as the critical structural elements for the specific interaction with TOP3β to avoid the non-cognate interaction with TOP3α.