Topoisomerases ( English topoisomerase ) - a class of enzymes - isomerases that affect the DNA topology [1] . Topoisomerases are able to relax supercoiled DNA molecules by introducing single- or double-stranded breaks followed by reduction (ligation) [2] . However, in some cases, topoisomerases can introduce negative supercoils or catenans into DNA [3] .
Topoisomerases were first described by Harvard University professor James Wong [4] .
Topoisomerases, facilitating the unwinding of DNA chains in a double helix, play an important role in the processes of replication and transcription . The role of topoisomerases in the formation of chromatin loops during chromosome condensation has been shown [3] . The incorporation of viral DNA into host chromosomes and other forms of recombination also require the presence of topoisomerases [5] .
Content
- 1 Classification
- 1.1 Topoisomerase I
- 1.2 Topoisomerase II
- 1.3 Variety of topoisomerases
- 2 Medical significance
- 3 notes
- 4 See also
- 5 Literature
Classification
Depending on the mechanism of action, topoisomerases are divided into type I topoisomerases, introducing single-stranded breaks without energy consumption, and type II topoisomerases, introducing double-stranded breaks with ATP expenditure. A special place among topoisomerases is occupied by DNA gyrase , characteristic of E. coli Escherichia coli [2] .
The following table lists the main features of the various types of topoisomerases:
| Topoisomerase | IA | IB | IIA | IIB |
|---|---|---|---|---|
| The need for metal ions | Yes | No | Yes | Yes |
| ATP Dependence | No | No | Yes | Yes |
| Break | ots | ots | dts | dts |
| End of attachment | 5' | 3 ' | 5' | 5' |
| Change in the number of super-turns | ± 1 | ± 1 | ± 2 | ± 2 |
Topoisomerase I
( EC 5.99.1.2 ) are monomeric proteins . They relax DNA, introducing single-stranded breaks without the expense of ATP. The mechanism of this is as follows. The introduction of single-stranded breaks occurs due to the amino acid residue tyrosine , which carries out a nucleophilic attack of the phosphate group of DNA, forming phosphotyrosine [6] . In this case, the enzyme itself binds to the released 3'- or 5'-end of the chain. Depending on which end topoisomerase joins, secrete:
- IA-type topoisomerases that bind to the 5'-end; remove only negative supercoiling;
- IB-type topoisomerases binding to the 3'-end [7] ; remove both positive and negative supercoiling [2] .
Such a mechanism of action does not require energy consumption, that is, ATP is not consumed during the operation of type I topoisomerases [6] . The number of turns in this case changes by 1 [3] .
The first type I topoisomerase, as already noted, was isolated in E. coli cells . In 1972, topoisomerases of this type were found in mammalian cells, and subsequently in yeast cells. Type I topoisomerases are known in archaea, for example, IA-topoisomerase of the thermophilic archaea Desulfurococcus amylolyticus , as well as in some viruses, for example, smallpox virus [7] .
Topoisomerase II
( EC 5.99.1.3 ) function in prokaryotes in the form of tetramers, in eukaryotes in the form of dimers . They carry out ATP-dependent cleavage of both DNA strands, followed by chain transfer through the gap and its ligation. The rupture occurs due to tyrosine topoisomerase binding to DNA with the formation of two 5'- phosphodiester bonds . Another double-stranded DNA passes into the resulting gap. Thus, the number of positive or negative supercoils changes by 2 (and not by 1, as in topoisomerases I). So, topoisomerases II can catenate and decatenate DNA nodes. DNA gyrase belonging to this type introduces negative supercoils [8] .
Topoisomerases II, as well as topoisomerases I, are divided into 2 groups: IIA and IIB . However, an analysis of the structures of topoisomerases IA, IIA, and IIB revealed their great structural similarity, in particular, the presence of a special fold for binding to metal ions [9] .
Variety of topoisomerases
The following table summarizes topoisomerases from various classes isolated from various organisms [9] .
| Topoisomerase | Type of | Organism | Size (kDa) and subunit structure | Features |
|---|---|---|---|---|
| Bacterial topoisomerase I (ω-protein) | IA | Bacteria (including E. coli ) | 97; monomer | Unable to relax positive superwitches |
| Eukaryotic topoisomerase I | IB | Eukaryotes (including humans) | 91; monomer | Can relax both positive and negative superwitches |
| Cowpox virus topoisomerase I | IB | Vaccinia virus | 37; monomer | ATP stimulates enzyme activity |
| Topoisomerase III | IA | Bacteria (including E. coli ) | 73; monomer | Has strong decenching activity |
| Reverse gyrase | IA | Thermophilic archaea (including Sulfolobus acidocaldarius | 143; monomer | ATP-dependently can add positive supercoils to DNA |
| DNA gyrase | IIA | Bacteria (including E. coli ), some lower eukaryotes | 97 and 99 A 2 B 2 | Can ATP-add negative supercoils to DNA |
| T4 topoisomerase | IIA | Phage T4 | 58, 51 and 18; 2 copies of each subunit | It relaxes DNA but does not supercoil (ATP-dependent) |
| Eukaryotic topoisomerase II | IIA | Eukaryotes (including humans) | 174; homodimer | It relaxes DNA but does not supercoil (ATP-dependent) |
| Topoisomerase IV | IIA | Bacteria (including E. coli ) | 84 and 70 C 2 E 2 | Relaxes DNA, but does not supercoil, strong decatenase (ATP-dependent) |
| Topoisomerase VI | IIB | Archaea (including Sulfolobus shibatae ) | 45 and 60 A 2 B 2 | It relaxes DNA but does not supercoil (ATP-dependent) |
Medical Importance
Topoisomerases play an important role in cell growth and division processes, and therefore they are often targets of various drugs [9] - .
So, DNA gyrase and topoisomerase IV close to it are targets of two main groups of antibacterial drugs: quinolones and coumarins . Quinolones (including nalidixic acid and ciprofloxacin ) supposedly block the rupture and ligation stage in the work of gyrase. Coumarins (including and ) act completely differently: they block the hydrolysis of ATP by gyrase [9] .
Eukaryotic topoisomerases are also targets of many drugs, in particular, antitumor drugs. For example, the anti-cancer drug , whose derivatives are widely used in anti-cancer chemotherapy , acts on human topoisomerase I in the same way that quinolones act on gyrase [9] .
In addition to the fact that topoisomerases can be targets of antibiotics and antitumor drugs, they can also act as targets of toxins . So, the bacterial toxin Ccdb acts on gyrase. Ccdb is a small protein weighing 11.7 kDa. It is part of the toxin-antitoxin system, forming a complex with another protein - Csda, and plays a role in the stabilization of the E. coli F plasmid . The loss of the F plasmid leads to the loss of a relatively unstable Csd. As a result, Ccdb is released, blocks gyrase and thereby kills the host cell. Studying the mechanism of action of such toxins may give new ideas for the development of new gyrase inhibitors [9] .
The following table provides information on various topoisomerase inhibitors [9] :
| Inhibitor | Target Isomerase | Therapeutic effect |
|---|---|---|
| Quinolones (including ciprofloxacin ) | DNA gyrase and topoisomerase IV | Effective antibacterial agents |
| Coumarins (including ) | DNA gyrase and topoisomerase IV | Antibiotics , but not widely used |
| (including topotecan ) | Human topoisomerase I | Anticancer drugs |
| Human topoisomerase II | Anticancer drugs | |
| Podophyllotoxins (including teniposide ) | Human topoisomerase II | Anticancer drugs |
Notes
- ↑ Champoux JJ DNA topoisomerases: structure, function, and mechanism (Eng.) // Annu. Rev. Biochem. : journal. - 2001. - Vol. 70 . - P. 369-413 . - DOI : 10.1146 / annurev.biochem.70.1.369 . - PMID 11395412 .
- ↑ 1 2 3 Konichev, Sevastyanova, 2012 , p. 99.
- ↑ 1 2 3 Konichev, Sevastyanova, 2012 , p. one hundred.
- ↑ National Academy of Sciences: NAS Award in Molecular Biology . National Academy of Science. Date of treatment January 7, 2009. Archived March 22, 2012.
- ↑ Zhimulev I.F. General and molecular genetics. - 1. - Novosibirsk: Publishing House of the Novosibirsk University, 2002. - 459 p. - 2000 copies. - ISBN 5761505096 .
- ↑ 1 2 Molecular biology and genetics. Explanatory Dictionary: DNA-relaxing enzymes .
- ↑ 1 2 D.V. Bugreev, G.A. Nevinsky . The structure and mechanism of action of IA type topoisomerases // Successes in Biological Chemistry. - 2009 .-- T. 49 . - S. 129-158 . Archived March 21, 2014.
- ↑ Konichev, Sevastyanova, 2012 , p. 99-100.
- ↑ 1 2 3 4 5 6 7 DNA topoisomerases .
See also
- DNA replication
Literature
- James C. Wang (2009) Untangling the Double Helix. DNA Entanglement and the Action of the DNA Topoisomerases , Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, 2009. 245 pp. ISBN 9780879698799
- Konichev A.S., Sevastyanova G.A. Molecular biology. - Publishing Center "Academy", 2012. - 400 p. - ISBN 978-5-7695-9147-1 .