Wikipedia

User:Hhuss/sandbox

< User:Hhuss
Exonuclease III
Crystal structure of exonuclease III
from E. coli.[1][2]
Identifiers
OrganismE. coli strain K-12/MG1655
SymbolxthA
Alt. symbolsExoIII
Entrez946254
RefSeq (Prot)NP_416263
UniProtP09030
Other data
EC number3.1.11.2
Chromosomegenome: 1.83 - 1.83 Mb
Search for
StructuresSwiss-model
DomainsInterPro

Exonuclease III (ExoIII) is an enzyme that belongs to the exonuclease family. ExoIII catalyzes the stepwise removal of mononucleotides from 3´-hydroxyl termini of double-stranded DNA.[1] A limited number of nucleotides are removed during each binding event, resulting in coordinated progressive deletions within the population of DNA molecules.[2]

Function

edit

The preferred substrates are blunt or recessed 3´-termini, although ExoIII also acts at nicks in duplex DNA to produce single-strand gaps. It is a 3' to 5' exonuclease.[3] The enzyme is not active on single-stranded DNA, and thus 3´-protruding termini are resistant to cleavage. The degree of resistance depends on the length of the extension, with extensions 4 bases or longer being essentially resistant to cleavage. This property is used to produce unidirectional deletions from a linear molecule with one resistant (3´-overhang) and one susceptible (blunt or 5´-overhang) terminus.[4]

ExoIII activity depends partially on the DNA helical structure [5] and displays sequence dependence (C>A=T>G).[6] ExoIII is an enzyme that repairs DNA using AP site (apurinic/apyrimidic) bonding only if the uracil is removed from the DNA sequence. [7] This function on the AP site can also be used to cleave phosphodiester bonds in order to produce 5'-termini. The 3' hydroxyl group catalyzes the separation of mono nucleotides on the 5' end to denature the DNA sequence.[8]

ExoIII has also been reported to have RNase H, 3´-phosphatase and AP-endonuclease activities.[1]

Regulation

edit

Temperature, salt concentration and the ratio of enzyme to DNA greatly affect enzyme activity, requiring reaction conditions to be tailored to specific applications.

References

edit
  1. ^ a b c 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.
  2. ^ a b Image rendered in MacPyMOL©2006 DeLano Scientific
  3. ^ Smith, A J (1979-3). "The use of exonuclease III for preparing single stranded DNA for use as a template in the chain terminator sequencing method". Nucleic Acids Research. 6 (3): 831–848. ISSN 0305-1048. PMID 440973. {{cite journal}}: Check date values in: |date= (help)
  4. ^ Rogers SG, Weiss B (1980). "Exonuclease III of Escherichia coli K-12, an AP endonuclease". Meth. Enzymol. Methods in Enzymology. 65 (1): 201–11. doi:10.1016/S0076-6879(80)65028-9. ISBN 978-0-12-181965-1. PMID 6246343.
  5. ^ Maniatis, Tom; Sambrook, Joseph; Fritsch, E. F. (1989). Molecular cloning: a laboratory manual (2nd ed.). Cold Spring Harbor, N.Y: Cold Spring Harbor Laboratory. pp. 5.84–5. ISBN 0-87969-309-6.
  6. ^ Henikoff S (June 1984). "Unidirectional digestion with exonuclease III creates targeted breakpoints for DNA sequencing". Gene. 28 (3): 351–9. doi:10.1016/0378-1119(84)90153-7. PMID 6235151.
  7. ^ Saporito, S M; Gedenk, M; Cunningham, R P (1989-5). "Role of exonuclease III and endonuclease IV in repair of pyrimidine dimers initiated by bacteriophage T4 pyrimidine dimer-DNA glycosylase". Journal of Bacteriology. 171 (5): 2542–2546. ISSN 0021-9193. PMID 2468648. {{cite journal}}: Check date values in: |date= (help)
  8. ^ Zhu, Yu Sheng; Isaacs, Stephen T.; Cimino, George D.; Hearst, John E. (1991). "The use of exonuclease III for polymerase chain reaction sterilization". Nucleic Acids Research. 19 (9): 2511–2511. doi:10.1093/nar/19.9.2511. ISSN 0305-1048.

Further reading

edit


Category:EC 3.1

Retrieved from "https://en.wikipedia.org/w/index.php?title=User:Hhuss/sandbox&oldid=872734250"