Topoisomerase II in Review

Topoisomerases are enzymes that help regulate the over-winding or under-winding of DNA. The winding can also lead to tangles or knots in the DNA that can inhibit and affect transcription processes and DNA replication. Because of their function in aiding in these problems, topoisomerases are vital enzymes in the body with unique and interesting chemistry.



This image is just a residue of topoisomerase II (PDB 1BJT). This is the core that binds to and cleaves the DNA (residues 409-1201). The spaces where DNA fits are apparent in this structure. Because this is only a residue, this is all one chain.



In this image (PDB 2RGR) we can see the same topoisomerase II residue as before, but now it is bound to the helical DNA (shown in pink and blue). Topoisomerase II helps relax super-coiling and repairs knots in the DNA by cutting through both strands and releasing tension.

Topoisomerases are enzymes that help regulate the over-winding or under-winding of DNA. The winding can also lead to tangles or knots in the DNA that can inhibit and affect transcription processes and DNA replication. Because of their function in aiding in these problems, topoisomerases are vital enzymes in the body with unique and interesting chemistry.

In the most simplest form, topoisomerases bind to the DNA to cut the phosphate backbone. Once the DNA is cut, it allows for the tension to be relieved or the knot to be released. After this occurs, the DNA backbone is resealed the the DNA is fixed.


(http://www.lookfordiagnosis.com/mesh_info.php?term=dna+topoisomerases%2C+type+i&lang=1)

There are two different types of topoisomerases that function in the body. Type I (as you can see in the above diagram) just cuts through one strand of the DNA. This "nick" functions best at just relieving tension, but wouldn't help with knots that occur. This is where the type II topoisomerase comes in handy. Type II cuts through both strands of the DNA, allows for an unbroken piece of DNA to go through the break, and then finally reseals the strands. This fixes knots that would be expected to occur with the condensation of DNA.

Class II topoisomerases require ATP to fix knots. When it binds to one part of the DNA (G-segment), it uses ATP to bind to another parts (T-segment). The topoisomerase cuts the G-segments to allow the T-segment to pass through the break and fix the problem of the knot. Then the G-segment is glued back together and the topoisomerase releases. You can see this occur in the figure below.


(http://www.udel.edu/chem/bahnson/chem645/websites/Sapra/Mechanism%20of%20type%20II%20topoisomerase.html)

Because of its uses, topoisomerase inhibitors are increasingly being used as anti-cancer drugs. When these drugs interfere with enzyme activity, the topoisomerase may not be able to fix knots, or it will break the DNA, but not reseal the ends. Both of these could be detrimental to the cells. Replication would be inhibited which is a feature of cancer cells. While no other disease is currently treated using topoisomerase II, future research could lead to new possibilities. 

As you can expect, topoisomerase II are very important in your body for normal replication and transcription. These enzymes are fascinating in their way of releasing knots by introducing double-stranded breaks. Cell survival is impacted by the function of these enzymes and they deserve to be protein of the year.


(http://en.wikipedia.org/wiki/Type_II_topoisomerase)




Sources:
Champoux JJ (2001). "DNA topoisomerases: structure, function, and mechanism". Annu. Rev. Biochem. 70: 369–413.

http://www.ebi.ac.uk/interpro/potm/2006_1/Page2.htm

Willmore E, de Caux S, Sunter NJ et al. (2004). "A novel DNA-dependent protein kinase inhibitor, NU7026, potentiates the cytotoxicity of topoisomerase II poisons used in the treatment of leukemia". Blood 103 (12): 4659–65.

The Beauty of Topoisomerase II

Topoisomerases are enzymes that help regulate the over-winding or under-winding of DNA. The winding can also lead to tangles or knots in the DNA that can inhibit and affect transcription processes and DNA replication. Because of their function in aiding in these problems, topoisomerases are vital enzymes in the body with unique and interesting chemistry.

In the most simplest form, topoisomerases bind to the DNA to cut the phosphate backbone. Once the DNA is cut, it allows for the tension to be relieved or the knot to be released. After this occurs, the DNA backbone is resealed the the DNA is fixed.


(http://www.lookfordiagnosis.com/mesh_info.php?term=dna+topoisomerases%2C+type+i&lang=1)

There are two different types of topoisomerases that function in the body. Type I (as you can see in the above diagram) just cuts through one strand of the DNA. This "nick" functions best at just relieving tension, but wouldn't help with knots that occur. This is where the type II topoisomerase comes in handy. Type II cuts through both strands of the DNA, allows for an unbroken piece of DNA to go through the break, and then finally reseals the strands. This fixes knots that would be expected to occur with the condensation of DNA.

Class II topoisomerases require ATP to fix knots. When it binds to one part of the DNA (G-segment), it uses ATP to bind to another parts (T-segment). The topoisomerase cuts the G-segments to allow the T-segment to pass through the break and fix the problem of the knot. Then the G-segment is glued back together and the topoisomerase releases. You can see this occur in the figure below.


(http://www.udel.edu/chem/bahnson/chem645/websites/Sapra/Mechanism%20of%20type%20II%20topoisomerase.html)

Because of its uses, topoisomerase inhibitors are increasingly being used as anti-cancer drugs. When these drugs interfere with enzyme activity, the topoisomerase may not be able to fix knots, or it will break the DNA, but not reseal the ends. Both of these could be detrimental to the cells. Replication would be inhibited which is a feature of cancer cells.

As you can expect, topoisomerase II are very important in your body for normal replication and transcription. These enzymes are fascinating in their way of releasing knots by introducing double-stranded breaks. Cell survival is impacted by the function of these enzymes and they deserve to be protein of the year.


(http://en.wikipedia.org/wiki/Type_II_topoisomerase)




Sources:
Champoux JJ (2001). "DNA topoisomerases: structure, function, and mechanism". Annu. Rev. Biochem. 70: 369–413.

http://www.ebi.ac.uk/interpro/potm/2006_1/Page2.htm

Willmore E, de Caux S, Sunter NJ et al. (2004). "A novel DNA-dependent protein kinase inhibitor, NU7026, potentiates the cytotoxicity of topoisomerase II poisons used in the treatment of leukemia". Blood 103 (12): 4659–65.

Topoisomerase in biochemical literature

Topoisomerase II is a vital part of DNA replication and maintenance. Even though it is known that topoisomerase II creates double strand breaks in the DNA to relieve super coiling or correct knots, more research is being done to understand this process and its role in the cell. The following articles address different aspects of what is currently known and what has yet to be learned about topoisomerase II.

Article 1: The Analysis of Mutant Alleles of Different Strength Reveals Multiple Functions of Topoisomerase 2 in Regulation of Drosophila Chromosome Structure

this figure shows the chromosome rearrangemnts that could result from problems with topo II (Figure 3 in article)

This article, posted in PLOS Genetics journal, states research done with topoisomerase II in Drosophila. Vertebrates contain two topo II isoforms and little is known about why there is this redundancy. In contrast, Drosophila (fruit flies) contain a single topo II enzyme and it is suitable to use for research that could be compared to the enzyme activity in vertebrates. Experiments were done in vivo with mutant flies that had minimally repressed, moderately repressed or no topo II activity. It was found that the mutant flies with even minimal reduced topo II activity exhibited "strong morphological abnormalities" and defects. Mutant flies of moderate topo II mutations frequently had chromosome breaks and rearrangements. When topo II was gone it resulted in anueploid and polyploid chromosomes with poorly condensed chromatin and broken chromosomes. These results confirm why topo II inhibitors are used in cancer chemotherapy. If the DNA is not repaired, the increasing damage could ultimately kill the cancer cells.

Mengoli, Valentina et al. “The Analysis of Mutant Alleles of Different Strength Reveals Multiple Functions of Topoisomerase 2 in Regulation of DrosophilaChromosome Structure.” Ed. Gregory P. Copenhaver. PLoS Genetics 10.10 (2014): e1004739. PMC. Web. 7 Mar. 2015.

Article 2: The DNA cleavage reaction of topoisomerase II: wolf in sheep's clothing

this figure (Figure 4 in article) demonstrates the necessity of topo II in the cell, but also the potential dangers and problems it could cause

This next article talked more about the process of DNA cleavage. Topo II is essential for almost every process of movement of DNA. It is known that the enzyme generates a double strand break. While this breaking of the DNA is vital, it could also harm the DNA by fragmenting the genome. The cleavage reaction that topo II is involved in is also thought to trigger translocations -- one specifically associated with certain types of leukemia. Topo II uses active site tyrosyl residues. It initiates DNA cleavage by using nucleophilic attack on the active site tyrosine of the phosphate backbone of DNA. Figure 2 of the article simplifies the process.

Besides the nucleophilic attack of tyrosine, little is known about the DNA cleavage details. Regardless, this process is important in the cell, but in excess, it could be detrimental. It is a balance. 

Deweese, Joseph E., and Neil Osheroff. “The DNA Cleavage Reaction of Topoisomerase II: Wolf in Sheep’s Clothing.” Nucleic Acids Research 37.3 (2009): 738–748. PMC. Web. 7 Mar. 2015.

Article 3: DNA cleavage and opening reactions of human topoisomerase IIα are regulated via Mg(2+)-mediated dynamic bending of gate-DNA

The previous article highlighted the idea that little is known about the process that controls and regulates the DNA cleavage, this article talks about the identification of a potential regulation mechanism. We know that there is a balance that needs to be met, so there must be some form of regulation and control. Through experiments, they were able to see that Mg(2+) ions induce a structural change of G-segment DNA, making it into a cleavageable (cleavage-competent) form. In addition, "bending" of the DNA helps coordinate the double-stranded breaks.

 Lee, Jung et al. "DNA Cleavage and Opening Reactions of Human Topoisomerase II are Regulated via MG(2+)-Mediated Dynamic Bending of Gate-DNA". PNAS 109.8 (2012). 

The Many Images of Topoisomerase II

This image is just a residue of topoisomerase II (PDB 1BJT). This is the core that binds to and cleaves the DNA (residues 409-1201). The spaces where DNA fits are apparent in this structure. Because this is only a residue, this is all one chain.

This image is the same topoisomerase residue as above (PDB 1BJT), but here you can see the helices and sheets that make up this residue. Again, this is all one chain and the color represents that.

In this image (PDB 2RGR) we can see the same topoisomerase II residue as before, but now it is bound to the helical DNA (shown in pink and blue). Topoisomerase II helps relax super-coiling and repairs knots in the DNA by cutting through both strands and releasing tension.

This next image (PDB 2RGR) shows the residue that binds to the DNA and the DNA molecule as well. When the colors are sorted by chain, you can see the doubled-stranded helical DNA in pink and blue and the chain in green is the topoisomerase II.

In this final image (PDB 1BJT), we can see the topoisomerase II residue not bound to the DNA.