Exonuclease III

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Exonuclease III
Crystal structure of exonuclease III
from E. coli.[1][2]
Organism E. coli strain K-12/MG1655
Symbol xthA
Alt. symbols ExoIII
Entrez 946254
RefSeq (Prot) NP_416263
UniProt P09030
Other data
EC number
Chromosome genome: 1.83 - 1.83 Mb

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]


The preferred substrates are blunt or recessed 3´-termini, although ExoIII also acts at nicks in duplex DNA to produce single-strand gaps. 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.[3]

ExoIII activity depends partially on the DNA helical structure [4] and displays sequence dependence (C>A=T>G).[5]

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


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


  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. ^ 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. 
  4. ^ 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. 
  5. ^ 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. 

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