The Oncologist, Vol. 7, No. 4, 381-382,
August 2002
© 2002 AlphaMed Press
FUNDAMENTALS OF CANCER MEDICINE |
The Molecular Perspective: DNA Topoisomerases
David S. Goodsell
Correspondence:
David S. Goodsell, Ph.D., Associate Professor, The Scripps Research Institute, Department of Molecular Biology, 10550 North Torrey Pines Road, La Jolla, California 92037, USA. Telephone: 858-784-2839; Fax: 858-784-2860; e-mail: goodsell{at}scripps.edu Website:http://www.scripps.edu/pub/goodsell
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LEARNING OBJECTIVES
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After completing this course, the reader will be able to:
- Gain a basic understanding of the structure and function of the DNA topoisomerases and their place as targets for chemotherapy.
Access and take the CME test online and receive one hour of AMA PRA category 1 credit at CME.TheOncologist.com
Each cell in your body contains about two meters of DNA, all bundled into a space a million times smaller. As you might imagine, this causes significant problems when cells manipulate their DNA, while accessing the genomic information and when dividing the DNA into two portions during cell division. To make things even more complicated, the DNA is a double helix, so it must be unwound to access its information. If you have ever tried to unravel the individual fibers in a rope, you will understand the challenges that this imposes.
All living cells have a set of special enzymes, the DNA topoisomerases, that deal with these topological problems. There are two basic types that solve two major topological problems. Class I topoisomerases, shown in Figure 1
, solve the problems caused by the helical nature of DNA. They grasp the DNA and make an incision, cutting the strand but keeping a firm grip on one of the severed ends. The gapped helix is then free to rotate around the other strand, releasing any strain that may be present from overwinding or underwinding. Once relaxed, the topoisomerase reconnects the broken strand. DNA topoisomerase I plays an essential role in DNA replication and DNA transcription. In both cases, the DNA must be unwound to allow reading of the information held inside. Topoisomerase performs its duty nearby, releasing the stresses that occur in the process.
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Figure 1. Type I topoisomerase (in green) is a monomeric enzyme that wraps around the DNA double helix (pink and yellow), as shown on the left. The active site is shown in more detail below, by removing the portion of the protein in front of the DNA. A key tyrosine residue (in red) cleaves the DNA strand and forms a covalent bond with the DNA phosphate on one side of the gap (the phosphate is bright red and yellow). This leaves a free end on the other side of the gap, marked here with a star, that is free to rotate around the opposite strand. After the topological tension is relaxed, the DNA backbone is resealed. Coordinates were taken from entry 1ei1 at the Protein Data Bank (http://www.pdb.org).
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The class II topoisomerases, shown in Figure 2, perform an even more remarkable feat involving the juggling of two DNA strands. These topoisomerases grab a DNA double helix and break both strands, retaining a firm grip on each half. Then, a second DNA strand is passed through the gap. Finally, the first DNA is resealed behind it. Topoisomerase II plays an essential role in cell division, as the chromosomes are segregated into the two daughter cells. It releases any loops and tangles that may be linking the two chromosomes together as they separate.
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Figure 2. Type II topoisomerase is a dimeric enzyme with a large central hole. It is thought to be a highly dynamic structure with two "gates" of entry for DNA into this hole. In one proposed mechanism, a DNA double helix enters and is cleaved on both strands, forming covalent bonds with two tyrosines (shown in red). The second DNA strand then passes in the top, through the gap in the DNA, and out the bottom. The first DNA strand is then resealed behind it. This structure is modeled after two sets of coordinates, taken from PDB entries 1bgw and 1a31.
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Some of the most commonly employed antitumor drugs attack the topoisomerases, taking advantage of their key role in cellular information flow. The anthracyclines, such as doxorubicin and daunorubicin, attack type II topoisomerases, and compounds based on the plant toxin campothecin attack type I topoisomerases. In both cases, the drugs bind to the complex of DNA and topoisomerase after the incisions have been made, blocking the reaction that reseals the DNA. The binding of the drug is reversible, so if the drug then unbinds, the topoisomerase can finish its job and everything is fine. But in some cases, a neighboring replication fork runs into the blocked topoisomerase, causing the release of a piece of the gapped DNA strand that is not chemically held by the topoisomerase. The result is breakage of the DNA, resulting in death of the cell.
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ADDITIONAL READING
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- Li TK, Liu LF. Tumor cell death induced by topoisomerase-targeting drugs. Annu Rev Pharmacol Toxicol 2001;41:53–77.[CrossRef][Medline]
- Wang JC. Cellular roles of DNA topoisomerases: a molecular perspective. Nat Rev Mol Cell Biol 2002;3:430–440.[CrossRef][Medline]
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