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Human Topoisomerase I and DNA Complex

Nat Fox '16 and Yohanna Ewing '16


Contents:


I. Introduction

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Human Topoisomerase I (topo I) is a nuclear protein that relieves the tension in overwound DNA helices, a result of the transcription and translation processes.1 This unwinding process is critical for proper DNA replication, transcription, and maintenance, making Topoisomerase I a vitally important protein. Topo I achieves DNA relaxation by making a cut to one strand of the double helix. The catalytic nucleophilic tyrosine (Tyr 723) attacks the electrophilic phosphodiester DNA backbone introducing a break in the strand and forming a covalent bond between broken strand and the protein. This allows the free end of the strand to rotate in a "Controlled Rotation" manner, relieving helix tension1. The goal of this tutorial is to illustrate how topo I binds to DNA and carries out the chemical reactions required for DNA relaxation.  
 

II. General Structure

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Topo I is a heterodimer composed of 4 domains: the N-terminus, core (subdomain I, subdomain II, and subdomain III), C-terminal domain, and the linker domain.1. The N-terminus domain, not pictured, is highly charged and thought to be unstructured. Core subdomains I and II contain the CAP (residues 202-434) and subdomain III contains the CAT (residues 435-635) which the double stranded DNA and position the active site around the target phosphate group.2 Core subdomain III contains three of the amino acids (His632, Arg590, and Arg488) involved in the active site. The C-terminal domain contains the catalytic tyrosine and alpha-21 helix necessary for the formation of the active complex. The topo I dimer is the result of the three salt bridges and nine hydrophobic pairwise interactions formed between alpha helices, alpha-18 and alpha-19, in the linker domain.2


III. DNA Binding


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DNA binding of topo I to the dsDNA is the result of a coulombic protein/DNA charge interaction (positive=blue, neutral=white, negative=red) between the positively charged CAP CAT and the linker domain with the negatively charged sugar-phosphate backbone.1 Topo 1 initiates its transition into the active state when the CAP and CAT regions encircle and bind to the DNA. This DNA/protein interaction shift the alpha helix residues Thr597 and Leu602 of alpha-16 and Val626, Leu629, and Cys630 of alpha-17 of the CAT and catalytic Tyr723 of alpha-21 of the C-terminal domain to create the binding where catalytic Tyr723 is rotated from buried to active position.2 Lys650 and Arg708 make hydrogen bonding with phosphates on the target cut strand. These residues bond 9-10 nucleotides from the cleavage site on the scissile strand and 7 to 10 nucleotides on the intact strand which further stabilizes the active site. The linker domain contains an additional seven positively charged and seven polar residues that do not directly interact with the sugar-phosphate backbone. These residues likely play a role in the "controlled rotation" mechanism of human topoisomerase I.1


IV. DNA Cleavage


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Once the catalytic tyrosine is in position, DNA cleavage is carried out by a nucleophilic attack. The hydroxyl group on Tyr723 attacks the electrophilic phosphate on the sugar-phosphate backbone. This results in a covalent bond between Tyr723 and the 3' end of the cleaved strand.1 The hydroxyl group binds to the phosphate to form a five substituent transition state which is stabilized by hydrogen bonds between water and the hydroxyl group of Tyr723 . Click for Mechanism.  This results in a covalent bond between Tyr723 and the 3' end of the cleaved strand. The hydroxyl group binds to the phosphate to form a five membered transition state which is stabilized by hydrogen bonds between water and the hydroxyl group of Tyr723 . Additionally, this hydrogen bonding induces a more basic nucleophile, increasing the rate of the reaction. The phosphate is held in place by hydrogen bonding between Oxygen 1 (O1) and Arg488, O1 and Arg590, and His623 and O2. Additionally, His632 acts as an acid by donating a proton to O5, the leaving group. DNA relaxation results from the the rotation of the free end (O5) of broken sugar-phosphate backbone around the intact strand of DNA.6 Mutations in these amino acids result in a nonfunctional active site.


V. Implications


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Human topoisomerase I is a popular target of anticancer therapies and research because of its important role in transcription and translation.3 Camptothecins, indolocarbazoles and indenoisoquinolines are the three major classifications of topo I specific therapies.4 These molecules interfere with the catalytic Tyr723 in the binding pocket to form a DNA lesion.3 The mechanism for topoisomerase inhibition is best understood in camptothecins, the first group of topo I specific compounds discovered. Camptothecins are planer pentacyclical molecules with a alpha-hydroxyacetone.3 When there is a guanine base on the 5' end of the broken DNA strand, the drug is able to bind to the DNA/protein which results in a ternary complex. This complex is stabilized by base stacking between the cyclical campothecin and guanine. The stabilized complex forms a DNA lesion which holds the DNA/topo I the intermediate cleaving position inhibiting cancerous cell proliferation.3 Different topo I inhibitors are effective in particular cancerous cell types. As of 2006, two camptothecin derived anti-cancer drugs have been approved by the Federal Drug Administration: Topotecan (Hycamin) targets ovarian and lung cancers and irinotecan (CPTII, Campto) targets colon cancer.3 These targeted therapies are more successful than traditional chemotherapy and have higher cure rate.5 Therefore, understanding human topoisomerase DNA/protein binding interaction can lead to more targeted specific therapies and higher remission and cure rates.

VI. References

1. Stewart, Lance, Matthew R. Redinbo, Xiayang Qui, Wim G.J. Hol, and James J. Champoux. 1998. A Model for the Mechanism of Human Topoisomerase I. Science 279, 1534-1541.
2. Lesher, Diem-Thu T., Yves Pommier, Lance Stewart, and Matthew R. Redinbo. 2002. 8-Oxoguanine Rearranges the Active Site of Human Topoisomerase I. PNAS 99 (19):12102-12107.
3. Moisan, F., Longy, M., Robert J, and. Morvan V. Le. 2006. Identification of Gene Polymorphisms of Human DNA Topoisomerase I in the National Cancer Institute Panel of Human Tumour Cell Lines. British Journal of Cancer 99(7)  
4. Moukharskaya J. 2012. Topoisomerase 1 Inhibitors and Cancer Therapy. Hematology/oncology clinics of North America. 26:507-507.
5. Arakawa, Yasuhiro, Koji Ozaki, Yutaka Okawa, and Hisashi Yamada. 2013. Three Missense Mutations of DNA Topoisomerase I in Highly Camptothecin-Resistant Colon Cancer Cell Sublines. Oncology Reports 30. 1053-1058  

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