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| Exonuclease III | |||||||
|---|---|---|---|---|---|---|---|
 | |||||||
| Identifiers | |||||||
| Organism | |||||||
| Symbol | xthA | ||||||
| Alt. symbols | ExoIII | ||||||
| Entrez | 946254 | ||||||
| RefSeq (Prot) | NP_416263 | ||||||
| UniProt | P09030 | ||||||
| Other data | |||||||
| EC number | 3.1.11.2 | ||||||
| Chromosome | genome: 1.83 - 1.83 Mb | ||||||
| |||||||
Introduction
[edit]Exonuclease’s are enzymes diverse in terms of substrate specificity, biochemical properties, and have specialized biological functions. They work in the cellular level by repairing DNA, have roles genetic recombination, help avoid mutations, hydrolyze phosphodiester bonds in DNA from a free end and provide genome stability. [3]
Structure
[edit]The structure of exonuclease III was created using an atomic model that was determined by fitting the amounts of three isomorphous heavy atom derivatives into an electron density map. [4] Exonuclease III is a compact of alpha,beta-protein. [4] There are beta-pleated sheets that are anti-parallel and have looped regions where they are linked. These are then surrounded by four alpha helices. The alpha helices form the outside layers of the fold, while the beta sheets form the hydrophobic core. [4]
Function
[edit]Exonuclease III is an exodeoxyribonuclease that is a part of the exonuclease family. The large family includes with individuals following the species names, I, III, IV, V, VII. The purpose of the enzyme is to excise mutagenic or toxic strands of DNA[5]. In order to carry out this function the enzyme must delete overhanging nucleotides from the overhanging 3' end of a helical DNA strand.[6] The enzyme is able to initiate the repair process of DNA pieces using specific site directed mutagenesis. [7]ExoIII functions by using a method that repairs DNA using AP Site bonding.[8] This function on the AP site can also be used to cleave phosphodiester bonds in order to produce 5'- termini in the place of what used to be a 3' end. In preforming this action, the enzyme has activated a blocked end of the DNA fragment and prepared it repair. [9]
While ExoIII has many functions it is limited in certain aspects as the enzyme is unable to act on 3' ends that contain more than 4 bases in length, ssDNA or thioester-linked nucleotides.
Regulation
[edit]In order to be used, temperature, ionic strength, template sequence and concentration of enzyme to DNA ratio has great effect on the enzyme. When used under specific, controlled conditions the reaction generally proceeds at uniform rates, this makes the enzyme yield rate predictable and ideal for reproduction of tests.[10] ExoIII can be rendered inactive by heating the enzyme to 65° celsius for 15 minutes.
Current Studies
[edit]There are many different exonuclease’s and many are still to be discovered in bacteria, current studies are being conducted in E. coli. Many exonuclease’s fall into superfamilies with different domains of life proving that exonuclease III has shown to be ancient. Exonuclease’s evolved early in the history of life and have vital biological roles. [11] Exonuclease III is specifically being studied for its activity and function, the current study conducted by Gachon University investigates the detection of endonuclease III using DNA-templated copper nanoclusters (DNA-CuNCs). The study showed that this enzyme is affected by the concentrations of magnesium and sodium ions. [12]
The applications of this enzyme can produce unidirectional nested deletions, site-directed changes, production of strand-specific labelled areas for site mutagenesis, and preparation of single-stranded substrates for sequencing. [13] This enzyme is used to prepare deletions on the ends of single stranded DNA fragments that are to be used for further study. [14] Studies like these are important because they can be used to detect diseases and may aid in finding better treatments or cures.
References
[edit]- ^ PDB: 1ako; Mol CD, Kuo CF, Thayer MM, Cunningham RP, Tainer JA (March 1995). "Structure and function of the multifunctional DNA-repair enzyme exonuclease III". Nature. 374 (6520): 381–6. doi:10.1038/374381a0. PMID 7885481.
- ^ Image rendered in MacPyMOL©2006 DeLano Scientific
- ^ https://www.ncbi.nlm.nih.gov/pubmed/26442508
- ^ a b c Kuo, C. F.; Mol, C. D.; Thayer, M. M.; Cunningham, R. P.; Tainer, J. A. (1994-07-29). "Structure and function of the DNA repair enzyme exonuclease III from E. coli". Annals of the New York Academy of Sciences. 726: 223–234, discussion 234–235. ISSN 0077-8923. PMID 8092679.
- ^ Hadi, Masood Z.; Wilson, David M. (2000-01-01). "Second human protein with homology to the Escherichia coli abasic endonuclease exonuclease III". Environmental and Molecular Mutagenesis. 36 (4). doi:10.1002/1098-2280(2000)36:4%3C312::aid-em7%3E3.0.co;2-k. ISSN 1098-2280.
- ^ 1969-, Casali, Nicola. Preston, Andrew, (2003). E. coli plasmid vectors : methods and applications. Humana Press. ISBN 9781592594092. OCLC 54464053.
{{cite book}}:|last=has numeric name (help)CS1 maint: extra punctuation (link) CS1 maint: multiple names: authors list (link) - ^ Slaitas, A.; Ander, C.; Földes-Papp, Z.; Rigler, R.; Yeheskiely, E. (2003-10). "Suppression of Exonucleolytic Degradation of Double-Stranded DNA and Inhibition of Exonuclease III by PNA". Nucleosides, Nucleotides and Nucleic Acids. 22 (5–8): 1603–1605. doi:10.1081/ncn-120023044. ISSN 1525-7770.
{{cite journal}}: Check date values in:|date=(help) - ^ Vandeyar, Mark A.; Weiner, Michael P.; Hutton, Carolyn J.; Batt, Carl A. (1988-05). "A simple and rapid method for the selection of oligodeoxynucleotide-directed mutants". Gene. 65 (1): 129–133. doi:10.1016/0378-1119(88)90425-8. ISSN 0378-1119.
{{cite journal}}: Check date values in:|date=(help) - ^ Demple, B.; Johnson, A.; Fung, D. (1986-10-01). "Exonuclease III and endonuclease IV remove 3' blocks from DNA synthesis primers in H2O2-damaged Escherichia coli". Proceedings of the National Academy of Sciences. 83 (20): 7731–7735. doi:10.1073/pnas.83.20.7731. ISSN 0027-8424. PMID 2429316.
- ^ "Thermo Fisher Scientific - US". www.thermofisher.com. Retrieved 2018-11-26.
- ^ https://www.ncbi.nlm.nih.gov/pubmed/26442508
- ^ https://www.ncbi.nlm.nih.gov/pubmed/30369112#
- ^ C., Dubey, R. (2014). Advanced biotechnology : For B Sc and M Sc students of biotechnology and other biological sciences. New Delhi: S Chand. ISBN 9788121942904. OCLC 883695533.
{{cite book}}: CS1 maint: multiple names: authors list (link) - ^ "Epicentre (an Illumina company)". www.epibio.com. Retrieved 2018-11-26.
Further reading
[edit]- Richardson CC, Lehman IR, Kornberg A (January 1964). "A Deoxyribonucleic Acid Phosphatase-Exonuclease from Escherichia coli. II. Characterization of the Exonuclease activity" (PDF). J. Biol. Chem. 239 (1): 251–8. PMID 14114851.
- Linxweiler W, Hörz W (August 1982). "Sequence specificity of exonuclease III from E. coli". Nucleic Acids Res. 10 (16): 4845–59. doi:10.1093/nar/10.16.4845. PMC 320823. PMID 6752885.