All About Topoisomerase by Doctor-dr

by Microbiology Doctor-dr

Topoisomerase- Definition, Types, Structure, Functions, Mechanism

Isomerase enzymes help to make isomers of any biological component by producing or assisting in the formation of isomers. They aid in the rearranging of many biomolecules during the establishment or breaking of bonds. Isomerase enzymes include topoisomerase.

What is Topoisomerase?

Topoisomerase is a necessary enzyme that helps in DNA replication, chromosomal segregation, transcription, and recombination.

1.   J.C. Wang discovered it in the 1970s while working on Escherichia coli. The type I topoisomerase was the culprit.

2.   It aids in modifying the topology of DNA, as the name implies. It has the ability to increase or reduce the degree of DNA unwinding.

3.   Because it solely operates on DNA strands, it's also known as DNA topoisomerase.

4.   It is ineffective against RNA.

5.   The phosphodiester link in the backbone of DNA strands is broken by it. As the enzyme exits, new linkages are generated.

Important Terminologies

Twist (Tw): It is the total count of helical turns of the strands of DNA. 

Writhe (Wr): It is the total count of turns of the double helix of DNA crossing on itself that indicates the supercoils of DNA.

Linking Number: It is the total number or addition of twists and writhes in DNA.

Linking No. = Wr+Tw

Topoisomerase Types

There are two types of topoisomerases: 

1.   Type I Topoisomerase

2.   Type II Topoisomerase

1.  Type I Topoisomerase 

Type I Topoisomerase Definition

Form I topoisomerase is a single-stranded DNA-cutting type of topoisomerase. It isn't an ATP-dependent enzyme in any way (exception: Reverse Gyrase).

It primarily adds one to the linkage number.

Note that odd varieties of topoisomerases are classified as type I, whereas even types are classified as type II.

Type I Topoisomerase Structure

In the type IA, there are a number of different domains. It might be somewhere between I and IV. Domain I contains the Toprim domain. Domains III and IV contain HTH (Helix-Turn-Helix). The tyrosine residues may be found in domain III's HTH. With all three domains present at the bottom of the topoisomerase structure, it looks to be a lock.

The active site (tyrosine) interacts with the C-terminal domain, N-terminal domain, capping, and catalytic lobe in Type IB.

Type I Topoisomerase Types

It is divided into three categories:

Type IA topoisomerases

It attaches to the DNA's 5′ carbon end.

This kind of topoisomerase is related to E. coli topoisomerase I.

There are three sorts of it:

• Topo IA is a bacterium that may be found in eubacteria.
• Topo III is present in eukaryotes and eubacteria.
• Reverse Gyrase is seen in archaebacteria as well as eubacteria. It is the only type I topoisomerase that requires ATP to function.

(Topoisomerase is referred to as topoisomerase here.)

Type IB topoisomerases

It attaches to the DNA's 3′ carbon end. In one strand, it develops a nick. This kind of topoisomerase is similar to human topoisomerase I.

Type IC topoisomerases

There is just one type of topoisomerase in it, which is topoisomerase V. It attaches to the DNA's 3′ carbon end. It's a kind of archaebacterium. It demonstrates the rotational control system.

Type I Topoisomerase Mechanism of action

It usually happens when the following events happen at the same moment.

• Cutting a single strand of DNA: The topoisomerase's active region includes the amino acid tyrosine. The breaking of a DNA strand is favoured by the rupture of the phosphodiester bond and the production of an intermediate with a phospho-tyrinosyl linkage. The process of link creation and cleavage is identical to that of type II topoisomerase. Tyrosine can target the 3' or 5' carbon end of a molecule.
• Strand passing: The uncut DNA strand goes through the crack after the cleavage. The enzyme switches from closed to open conformation at this stage, allowing strands to pass through. In the case of type I, no ATP is used in the conformational shift.
•  Religation: The phosphate attached to tyrosine is attacked again by the OH of the ribose group of the previously split strand, causing the intermediate linkage of tyrosine to be removed and the cleaved strand to be rejoined. The enzyme is recovered for the following cycle by returning to its original state (closed conformation).

Type I Topoisomerase Functions

• In biological processes such as replication and transcription, they are involved in the elimination of supercoils of DNA.
• Assist in DNA relaxation.
• They aid in the recombination process by breaking strands.
• They are also involved in the chromosomal condensation process.
• The DNA strands must be free of interwinding during mitosis, which is accomplished by topoisomerase I. 

2.  Type II Topoisomerase

Type II Topoisomerase Definition

A form of topoisomerase that breaks both strands of DNA at the same time is known as Type II topoisomerase. This enzyme is ATP-dependent. The connecting number is increased by two.

Type II Topoisomerase Structure

In eukaryotes, topoisomerase IIA is made up of two identical monomers (A-A), but in prokaryotes, it is made up of heterotetramers (A2B2).

Only heterotetramers make up topoisomerase IIB.

The four domains of topoisomerase II are as follows:

• N-terminal ATPase domain
• The C-terminal domain is varied.
• DNA binding domain is centrally positioned.
• The toprim domain is a hundred-amino-acid conserved domain.

Type II Topoisomerase Types

There are two types of it:

Type IIA topoisomerases

Viruses and all biological organisms contain it. There are three types:

• Topo II: It is found in eukaryotes
• Topo IV: It is found in bacteria. It differs from Gyrase. It is not involved in DNA wrapping while Gyrase is involved in DNA wrapping and promoting negative supercoils.
• Gyrase: It is found in bacteria and some eukaryotes. It introduces negative supercoiling decreasing the linking number by two.

Type IIB topoisomerases

Topo VI, which may be found in archaea and certain plants, is included.

Type II Topoisomerase Mechanism of action

When ATP is hydrolyzed, the following happens.

• Cleaving of DNA chain: Tyrosine residues are found in the enzyme that cleaves the DNA chain. They disrupt the DNA chain by forming covalent connections with the DNA strands. The lone pair of electrons in the O-atom in tyrosine serve as a nucleophile, attacking the Phosphorus in DNA's phosphate. It causes a hydroxyl group to develop by transferring a link from phosphate to one of the O-atoms connected to the ribose sugar. As a result, the covalently linked tyrosine connected to phosphorus cleaves the phosphate-sugar backbone. The 5′-phospho-tyrinosyl protein-DNA linkage is the name for this type of connection.

The enzyme breaks a duplex by acting on both strands at the same time.

• Crossing of the intact strand through the gap: Another entire duplex strand travels through the space above the fractured duplex in this scenario. ATP is required for the conformational shift in the enzyme.
• Religation: It is accomplished by the 3′-OH of the separated strand's sugar attacking the phosphate group that has formed an intermediate connection with tyrosine. With tyrosine, it repels the link and repairs the broken bond, allowing it to rejoin. It occurs on both strands of the duplex, ligating them together. The enzymes revert to their original shape and the cycle continues. 

Type II Topoisomerase Functions

• It causes the chromosome to become more disentangled.
• It is engaged in the relaxing of DNA rather than the supercoiling of DNA.
• DNA gyrase encourages DNA to form negative supercoils.
• One of the most essential roles is that it changes the connecting number of loops in DNA by two units.

Topoisomerase Inhibition

Topoisomerase inhibitors are chemical components that can prevent topoisomerase from working.

They can disrupt the ligation stage of DNA, resulting in broken strands in the cell and cell death by apoptosis.

The notion of topoisomerase inhibition is applied in the creation of antibacterial medicines. Antibiotics of the class coumarins, such as novobiocin and coumermycin, interfere with ATP binding in type II topoisomerases in bacteria, causing death. It also comprises antibiotics from the quinolone family, which block the religation of nicked DNA strands in the topoisomerase working mechanism's last step

Inhibition of topoisomerase in humans can be caused by chemotherapeutic drugs used to treat cancer. They can stabilise the intermediate generated by the topoisomerase's tyrosine and DNA's phosphate.

Clinical Significance of Topoisomerase

Many drugs operate by interfering with bacteria's type II topoisomerases. Antibiotics with a broad spectrum of action, such as fluoroquinolones, are among these drugs. They have the ability to cause the topoisomerase to damage the DNA.

Some chemotherapy drugs, such as irinotecan and topotecan for type I and teniposide and etoposide for type II, target cancer cell topoisomerases and are referred to as topoisomerase inhibitors.

Anti-topoisomerase antibodies (also known as anti-scl-70 antibodies) are detected against the topoisomerase I antigen in the autoimmune condition Scleroderma.

Topoisomerase vs Helicase

Topoisomerase	Helicase
It is involved in the prevention of supercoiling of DNA i.e. decreases tension on the unwound strands.	It is involved in the unwinding of DNA strands.
It works on DNA only.	It works acts on DNA and RNA.
It attacks the phosphodiester bond in the backbone of DNA.	It attacks the Hydrogen bonds between the double strands.
Its two types are: Type I Topoisomerase Type II Topoisomerase	Its two types are: RNA helicase DNA helicase

Topoisomerase vs Gyrase

Topoisomerase	Gyrase
It includes different types of enzymes including Gyrase.	Gyrase is a type of topoisomerase.
It is a large class of enzymes.	It is a type within the sub-class of Type II topoisomerase.
It is present in both prokaryotes and eukaryotes.	It is mostly present in prokaryotes and only in some eukaryotes.
It maintains the topology of DNA by the combined functions of different types of enzymes. It includes both negative and positive supercoiling of DNA.	Its specific function is to introduce negative supercoiling in DNA strands rather than to remove them.
Topoisomerases may or may not be ATP-dependent.	Gyrase is an ATP-dependent type of topoisomerase.