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http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/94898完整後設資料紀錄
| DC 欄位 | 值 | 語言 |
|---|---|---|
| dc.contributor.advisor | 詹迺立 | zh_TW |
| dc.contributor.advisor | Nei-Li Chan | en |
| dc.contributor.author | 劉可婷 | zh_TW |
| dc.contributor.author | Ko-Ting Liu | en |
| dc.date.accessioned | 2024-08-21T16:21:01Z | - |
| dc.date.available | 2024-08-22 | - |
| dc.date.copyright | 2024-08-21 | - |
| dc.date.issued | 2024 | - |
| dc.date.submitted | 2024-08-12 | - |
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(2000) DNA topoisomerase IIbeta and neural development. Science, 287, 131-134. Yang, X., Saha, S., Yang, W., Neuman, K.C., and Pommier, Y. (2022) Structural and biochemical basis for DNA and RNA catalysis by human Topoisomerase 3beta. Nat Commun, 13, 4656. Yoshida, M.M., and Azuma, Y. (2016) Mechanisms behind Topoisomerase II SUMOylation in chromosome segregation. Cell Cycle, 15, 3151-3152. Yoshida, M.M., Ting, L., Gygi, S.P., and Azuma, Y. (2016) SUMOylation of DNA topoisomerase IIalpha regulates histone H3 kinase Haspin and H3 phosphorylation in mitosis. J Cell Biol, 213, 665-678. Zhang, M., Liang, C., Chen, Q., Yan, H., Xu, J., Zhao, H., Yuan, X., Liu, J., Lin, S., Lu, W., and Wang, F. (2020) Histone H2A phosphorylation recruits topoisomerase IIalpha to centromeres to safeguard genomic stability. EMBO J, 39, e101863. | - |
| dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/94898 | - |
| dc.description.abstract | DNA 拓樸異構酶在生物體中扮演重要角色，其活性特點在於能催化暫時並可逆的 DNA 斷裂，以解決細胞進行生理活動時產生的染色體拓樸結構問題。對第二型拓 樸異構酶而言，與 DNA 結合會促使其蛋白四級構形發生變化，形成結構具二維對 稱性的活性中心，以進行雙股 DNA 的切割及再接合。第二型拓樸異構酶包含多個 功能域(functional domains)，其活性中心之組裝需要各個功能域在結合 DNA 後發 生協同性的構形改變並移動至適當位置、以執行後續的催化步驟。例如，DNA 結 合會誘發 TOPRIM 功能域之位移及其與二價金屬離子的配位;WHD 功能域的相 對滑動能讓活性中心的酪胺酸更靠近 DNA 與二價金屬離子，從而進行可逆的轉酯 化反應(transesterification)。為了詳細了解此酵素切割活性中心組裝的結構機制， 我們利用 X 射線晶體學解出了人類第二型拓撲異構酶 Top2α 和 Top2β 之催化核心 的結構，並由此二結構呈現之特性推論其應處於具有生理意義的起始反應狀態。結 構分析顯示，TOPRIM 功能域會以 in trans 的方式、和另一個單體的 Tower 功能域 形成交互作用界面，而這個界面的形成會使得原先被遮蔽的 DNA-binding groove 完全裸露，使得蛋白能與 DNA 結合並起始反應。我們也發現以突變破壞 TOPRIM 和 Tower 的交互作用會顯著降低第二型拓撲異構酶與 DNA 的結合、進而影響其催 化活性。此外、若干與疾病相關或能導致抗藥性的突變亦出現於此交互作用介面， 這些結果進一步強化了 TOPRIM 和 Tower 的交互作用對第二型拓撲異構酶活性的必要性。當我們將此結構與其他已結合 DNA 的第二型拓撲異構酶結構進行疊合時，能明顯觀察到 DNA 結合能誘使 TOPRIM 功能域產生大幅度的位移，並使其在整 個催化過程中穩定的與 DNA 交互作用，讓蛋白能進行 DNA 切割、再接合並釋放。 值得注意的是，在結構中我們發現了先前從未被報導過的蛋白質與 DNA 作用方式: TOPRIM 功能域與 DNA 的交互作用中，有一被精氨酸加帽的α螺旋 C 端能與 DNA 骨架形成穩定的交互作用。鑑於α螺旋極性的特性，一般認為蛋白質只會使用帶有 正電的α螺旋 N 端與 DNA 作用，而本研究首次發現蛋白質能利用精氨酸加帽的 方式中合帶負電的α螺旋 C 端，使其能與 DNA 交互作用。突變分析進一步證實了 此保留性精氨酸對第二型拓撲異構酶的重要性，亦對此胺基酸為何在所有第二型 拓撲異構酶中皆存在提供了功能上的解釋。總結來說，本研究揭示了 Tower domain 可藉由穩定 TOPRIM domain 來促進 DNA-binding groove 的暴露，使第二型拓撲異 構酶能起始反應，並詳細探討 TOPRIM 的位移對於組合切割活性中心的組成機轉。 | zh_TW |
| dc.description.abstract | The ability to catalyze reversible DNA cleavage and religation is central to topoisomerases’ role in regulating DNA topology. In type IIA topoisomerases (Top2), the formation of its DNA cleavage-religation center is driven by DNA-binding-induced structural rearrangements. These changes optimally position key catalytic modules, such as the active site tyrosine of the WHD domain and metal ion(s) chelated by the TOPRIM domain, around the scissile phosphodiester bond to perform reversible transesterification. To understand this assembly process in detail, we report the catalytic core structures of human Top2α and Top2β in an on-pathway conformational state. This state features an in trans formation of an interface between the Tower and opposing TOPRIM domain, revealing a groove for accommodating incoming Gate-segment DNA, in turn committing the enzyme for the subsequent catalytic steps. We also found that mutations disrupting the interaction between TOPRIM and Tower significantly reduce the binding of Top2 to DNA, thereby affecting its catalytic activity. Furthermore, several disease-related mutations or that cause drug resistance also map to this interface, reinforcing the essential role of the TOPRIM-Tower interaction for Top2 function. Structural superimposition further unveils how subsequent DNA-binding-induced disengagement of the TOPRIM and Tower domains allows a firm grasp of the bound DNA for cleavage/religation. Notably, we identified a previously undocumented protein-DNA interaction, formed between an arginine-capped C-terminus of an α-helix in the TOPRIM domain and the DNA backbone, significantly contributing to Top2 function. This work uncovers a previously unrecognized role of the Tower domain, highlighting its involvement in anchoring and releasing the TOPRIM domain, thus priming Top2 for DNA binding and cleavage. | en |
| dc.description.provenance | Submitted by admin ntu (admin@lib.ntu.edu.tw) on 2024-08-21T16:21:01Z No. of bitstreams: 0 | en |
| dc.description.provenance | Made available in DSpace on 2024-08-21T16:21:01Z (GMT). No. of bitstreams: 0 | en |
| dc.description.tableofcontents | 口試委員會審定書 I
謝辭 II 摘要 III Abstract V Abbreviations VII Contents VIII List of Figures X List of Tables XI 1. Introduction 1 1.1. Masters of the DNA Realm: The Indispensable Functions and Taxonomic Classification of DNA Topoisomerases Across Diverse Species 2 1.1.1 Type I Tops: IA, IB and IC 5 1.1.2 Type II Tops: IIA and IIB 6 1.2 Structural Characterization and Catalytic Mechanisms of Type IIA Tops 11 1.2.1 Evolutionarily Conserved Domain Structures of Top2 12 1.2.2 The Least Conserved CTD of Top2: Determinant of Distinct Cellular Roles 13 1.3 The Catalytic Cycle of Top2: Unveiling the Two-Gate Mechanism for Strand-Passage 17 1.3.1 Role of Metal Ions in Top2: Dynamic Configuration of the One-Metal Cleavage 20 1.3.2 Role of ATP in Top2: Protecting Against Aberrant DSBs 21 1.4 Targeting Top2: Strategies and Therapeutic Implications 24 1.4.1 Catalytic Inhibitors: Impairment of Top2 Enzymatic Activity 24 1.4.2 Double-Edged Sword of Top2 Poisons: Induction of Cytotoxic DSBs 26 1.5 Specific aim 28 2. Methods and Materials 32 2.1 Construction, expression and purification of recombinant proteins 33 2.2 Protein crystallization 37 2.3 X-ray diffraction data collection and structure determination 38 2.4 Supercoil relaxation assay 39 2.5 Electrophoretic mobility shift assay (EMSA) 40 2.6 In vivo top2 termerature-sensitive (top2ts) complementation assay 41 3. Results 42 3.1 Structures of hTop2core Apo Forms: An on-pathway conformational state of eukaryotic Top2 competent for engaging G-segment DNA 43 3.2 Mutation-Induced Destabilization of the TOPRIM-Tower′ Interface Impairs the Catalytic Function of Top2 45 3.3 The Assembly of Top2’s DNA Cleavage-Religation Center Requires Extensive Rearrangement of Molecular Interfaces 50 3.4 Unveiling a previously unknown type of protein-DNA contact mediated by a conserved arginine in the TOPRIM-DNA interface 52 3.5 The arginine residue that caps the C-terminus of helix Bα9 and bridges the Bα9-DNA interaction is crucial for the catalytic and cellular function of Top2 54 4. Conclusion and Discussion 58 5. Figures 63 6. Tables 93 7. References 97 | - |
| dc.language.iso | en | - |
| dc.subject | DNA切割暨黏合活性中心 | zh_TW |
| dc.subject | TOPRIM功能域 | zh_TW |
| dc.subject | X射線晶體學 | zh_TW |
| dc.subject | 蛋白質構型改變 | zh_TW |
| dc.subject | 第二型拓樸異構酶 | zh_TW |
| dc.subject | macromolecular X-ray crystallography | en |
| dc.subject | protein conformational change | en |
| dc.subject | DNA cleavage/religation center assembly | en |
| dc.subject | TOPRIM domain | en |
| dc.subject | Type IIA topoisomerase | en |
| dc.title | 第二型拓樸異構酶其DNA切割暨黏合活性中心形成之結構機制 | zh_TW |
| dc.title | Structural insights into the assembly of type IIA topoisomerase DNA cleavage/religation center | en |
| dc.type | Thesis | - |
| dc.date.schoolyear | 112-2 | - |
| dc.description.degree | 博士 | - |
| dc.contributor.oralexamcommittee | 李弘文;徐駿森;冀宏源;吳權娟;林敬哲 | zh_TW |
| dc.contributor.oralexamcommittee | Hung-Wen Li ;Chun-Hua Hsu;Hung-Yuan Chi;Chyuan-Chuan Wu;Jing-Jer Lin | en |
| dc.subject.keyword | 第二型拓樸異構酶,X射線晶體學,蛋白質構型改變,DNA切割暨黏合活性中心,TOPRIM功能域, | zh_TW |
| dc.subject.keyword | Type IIA topoisomerase,macromolecular X-ray crystallography,protein conformational change,DNA cleavage/religation center assembly,TOPRIM domain, | en |
| dc.relation.page | 109 | - |
| dc.identifier.doi | 10.6342/NTU202404261 | - |
| dc.rights.note | 同意授權(全球公開) | - |
| dc.date.accepted | 2024-08-13 | - |
| dc.contributor.author-college | 醫學院 | - |
| dc.contributor.author-dept | 生物化學暨分子生物學研究所 | - |
| 顯示於系所單位： | 生物化學暨分子生物學科研究所 | |
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