What is Topoisomerase

Topoisomerases (type I: EC 5.99.1.2, type II: EC 5.99.1.3) are isomerase enzymes that act on the topology of DNA.
The double-helical configuration that DNA strands naturally reside in makes them difficult to separate, and yet they must be separated by helicase proteins if other enzymes are to transcribe the sequences that encode proteins, or if chromosomes are to be replicated. In so-called circular DNA, in which double helical DNA is bent around and joined in a circle, the two strands are topologically linked, or knotted. Otherwise identical loops of DNA having different numbers of twists are topoisomers, and cannot be interconverted by any process that does not involve the breaking of DNA strands. Topoisomerases catalyze and guide the unknotting of DNA by creating transient breaks in the DNA using a conserved Tyrosine as the catalytic residue.
Function



Topological problems

There are three main types of topology: supercoiling, knotting and catenation. When outside of replication or transcription, DNA needs to be kept as compact as possible and these three states help this cause. However when transcription or replication occur, DNA needs to be free and these states seriously hinder the processes. In addition, during replication, the newly replicated duplex of DNA and the original duplex of DNA become intertwined and need to be completely separated in order to ensure genomic integrity as a cell divides.

Classes

Topoisomerases can fix these topological problems and are separated into two types separated by the number of strands cut in one round of action:

* Type I topoisomerase cuts one strand of a DNA double helix and then reanneals the cut strand. Type I topoisomerases are subdivided into two subclasses: type IA topoisomerases which share many structural and mechanistic features with the type II topoisomerases, and type IB topoisomerases, which utilize a controlled rotary mechanism. Examples of type IA topoisomerases include topo I and topo III. Historically, type IB topoisomerases were referred to as eukaryotic topo I, but IB topoisomerases are present in all three domains of life. Interestingly, type IA topoisomerases form a covalent intermediate with the 5' end of DNA, while the IB topoisomerases form a covalent intermediate with the 3' end of DNA. Recently, a type IC topoisomerase has been identified, called topo V. While it is structurally unique from type IA and IB topoisomerases, it shares a similar mechanism with type IB topoisomerase.

* Type II topoisomerase cuts both strands of one DNA double helix, passes another unbroken DNA strand through it, and then reanneals the cut strand. It is also split into two subclasses: type IIA and type IIB topoisomerases, which share similar structure and mechanisms. Examples of type IIA topoisomerases include eukaryotic topo II, E. coli gyrase, and E. coli topo IV. Examples of type IIB topoisomerase include topo VI.

Both type I and type II topoisomerases change the linking number of DNA. Type IA topoisomerases change the linking number by one, type IB and type IC topoisomerases change the linking number by any integer, while type IIA and type IIB topoisomerases change the linking number by two.

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