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Gene Review

ECs3002  -  exonuclease

Escherichia coli O157:H7 str. Sakai

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Disease relevance of ECs3002


High impact information on ECs3002

  • We conclude that the epsilon-subunit of polymerase III holoenzyme has a special role in defining the accuracy of DNA replication, probably through control of the 3' leads to 5' exonuclease activity [6].
  • The binding of AddAB enzyme to the 3'-end of the chi(Bs)-specific ssDNA results in protection from degradation by exonuclease I. This protection is gradually reduced with time and lost upon phenol extraction, showing that the binding is non-covalent [7].
  • Based on these results and crystallographic evidence showing that the template-primer binds in a cleft between the exonuclease and DNA polymerase domains in family A DNA polymerases, we propose that conserved sequences within the spacer of pol gamma may position the substrate with respect to the enzyme catalytic domains [8].
  • The antiserum did not inhibit the major oocyte 5' --> 3' exonuclease activity [9].
  • The Klenow polymerase has a large (46 kDa) domain containing the polymerase active site and a smaller (22 kDa) domain containing the active site for the 3'----5' exonuclease [10].

Chemical compound and disease context of ECs3002


Biological context of ECs3002

  • Studies of the mode of action of RNase D indicate that it is an exonuclease which initiates hydrolysis at the 3'-terminus and removes 5'-mononucleotides in a random fashion [16].
  • Even without a proofreading exonuclease, Klenow polymerase has high frameshift fidelity relative to several other DNA polymerases, including eucaryotic DNA polymerase-alpha, an exonuclease-deficient, 4-subunit complex whose catalytic subunit is almost three times larger [10].
  • Three different small deletions were produced at a single Pvu 2 restriction site in E. coli 23S rDNA of plasmid pKK 3535 using exonuclease Bal 31 [17].
  • In addition, conserved sequence motifs, implicated in the 3'-5' exonuclease activity of E. coli DNA polymerase I and shared by various family A and B DNA polymerases, were also identified [18].
  • This finding suggests that the herpesvirus exonuclease may utilize the same metal-ion-mediated mechanism employed by DNA polymerase I. We also attempted to transfer each of the mutations into the herpesvirus genome using a marker rescue protocol [5].

Associations of ECs3002 with chemical compounds

  • However, the pyrophosphate-induced infidelity has a different specificity from, and is not competitive with, two experimental markers of 3'----5' exonuclease proofreading; i.e. the effects of the next nucleotide or the addition of deoxynucleoside monophosphates [19].
  • An exonuclease activity co-sediments with the pTP X Ad Pol complex during glycerol gradient centrifugation, and co-purifies with the 140,000-Da Ad Pol after dissociation of the pTP X Ad Pol complex with urea [20].
  • In the presence of adenosine 5'-O-(3-thiotriphosphate), recA protein also inhibits the action of exonuclease I on single-stranded DNA and of lambda exonuclease on double-stranded DNA [21].
  • With enzymes devoid or deficient in 3' greater than 5' exonuclease activity purines, particularly adenine, are preferentially added opposite the putative abasic site [22].
  • 5-Hydroxypyrimidine deoxynucleoside triphosphates are more efficiently incorporated into DNA by exonuclease-free Klenow fragment than 8-oxopurine deoxynucleoside triphosphates [23].

Other interactions of ECs3002


Analytical, diagnostic and therapeutic context of ECs3002


  1. Biochemical and physical characterization of exonuclease V from Escherichia coli. Comparison of the catalytic activities of the RecBC and RecBCD enzymes. Palas, K.M., Kushner, S.R. J. Biol. Chem. (1990) [Pubmed]
  2. Use of monoacetyl-4-hydroxyaminoquinoline 1-oxide to probe contacts between guanines and protein in the minor and major grooves of DNA. Interaction of Escherichia coli integration host factor with its recognition site in the early promoter and transposition enhancer of bacteriophage Mu. Panigrahi, G.B., Walker, I.G. Biochemistry (1991) [Pubmed]
  3. Exonuclease requirements for recombination of lambda-phage in recD mutants of Escherichia coli. Dermić, D., Zahradka, D., Petranović, M. Genetics (2006) [Pubmed]
  4. Streptococcus pneumoniae DNA polymerase I lacks 3'-to-5' exonuclease activity: localization of the 5'-to-3' exonucleolytic domain. Diaz, A., Pons, M.E., Lacks, S.A., Lopez, P. J. Bacteriol. (1992) [Pubmed]
  5. Mutations within conserved motifs in the 3'-5' exonuclease domain of herpes simplex virus DNA polymerase. Hall, J.D., Orth, K.L., Sander, K.L., Swihart, B.M., Senese, R.A. J. Gen. Virol. (1995) [Pubmed]
  6. Identification of the epsilon-subunit of Escherichia coli DNA polymerase III holoenzyme as the dnaQ gene product: a fidelity subunit for DNA replication. Scheuermann, R., Tam, S., Burgers, P.M., Lu, C., Echols, H. Proc. Natl. Acad. Sci. U.S.A. (1983) [Pubmed]
  7. The AddAB helicase/nuclease forms a stable complex with its cognate chi sequence during translocation. Chédin, F., Handa, N., Dillingham, M.S., Kowalczykowski, S.C. J. Biol. Chem. (2006) [Pubmed]
  8. Mutations in the spacer region of Drosophila mitochondrial DNA polymerase affect DNA binding, processivity, and the balance between Pol and Exo function. Luo, N., Kaguni, L.S. J. Biol. Chem. (2005) [Pubmed]
  9. Characterization of FEN-1 from Xenopus laevis. cDNA cloning and role in DNA metabolism. Bibikova, M., Wu, B., Chi, E., Kim, K.H., Trautman, J.K., Carroll, D. J. Biol. Chem. (1998) [Pubmed]
  10. The fidelity of DNA synthesis catalyzed by derivatives of Escherichia coli DNA polymerase I. Bebenek, K., Joyce, C.M., Fitzgerald, M.P., Kunkel, T.A. J. Biol. Chem. (1990) [Pubmed]
  11. Structure determination of protein-ligand complexes by transferred paramagnetic shifts. John, M., Pintacuda, G., Park, A.Y., Dixon, N.E., Otting, G. J. Am. Chem. Soc. (2006) [Pubmed]
  12. Elucidation of the metal-binding properties of the Klenow fragment of Escherichia coli polymerase I and bacteriophage T4 DNA polymerase by lanthanide(III) luminescence spectroscopy. Frey, M.W., Frey, S.T., Horrocks, W.D., Kaboord, B.F., Benkovic, S.J. Chem. Biol. (1996) [Pubmed]
  13. Selective affinity chromatography of DNA polymerases with associated 3' to 5' exonuclease activities. Lee, M.Y., Whyte, W.A. Anal. Biochem. (1984) [Pubmed]
  14. Escherichia coli DNA polymerase I: inherent exonuclease activities differentiate between monofunctional and bifunctional adducts of DNA and cis- or trans-diamminedichloroplatinum(II). An exonuclease investigation of the kinetics of the adduct formation. Bernges, F., Dörner, G., Holler, E. Eur. J. Biochem. (1990) [Pubmed]
  15. A versatile endonuclease IV from Thermus thermophilus has uracil-excising and 3'-5' exonuclease activity. Back, J.H., Chung, J.H., Park, J.H., Han, Y.S. Biochem. Biophys. Res. Commun. (2006) [Pubmed]
  16. Escherichia coli RNase D. Catalytic properties and substrate specificity. Cudny, H., Zaniewski, R., Deutscher, M.P. J. Biol. Chem. (1981) [Pubmed]
  17. Structural and functional analysis of Escherichia coli ribosomes containing small deletions around position 1760 in the 23S ribosomal RNA. Zweib, C., Dahlberg, A.E. Nucleic Acids Res. (1984) [Pubmed]
  18. A DNA polymerase from the archaeon Sulfolobus solfataricus shows sequence similarity to family B DNA polymerases. Pisani, F.M., De Martino, C., Rossi, M. Nucleic Acids Res. (1992) [Pubmed]
  19. On the fidelity of DNA synthesis. Pyrophosphate-induced misincorporation allows detection of two proofreading mechanisms. Kunkel, T.A., Beckman, R.A., Loeb, L.A. J. Biol. Chem. (1986) [Pubmed]
  20. Properties of the adenovirus DNA polymerase. Field, J., Gronostajski, R.M., Hurwitz, J. J. Biol. Chem. (1984) [Pubmed]
  21. Escherichia coli recA protein protects single-stranded DNA or gapped duplex DNA from degradation by RecBC DNase. Williams, J.G., Shibata, T., Radding, C.M. J. Biol. Chem. (1981) [Pubmed]
  22. Abasic sites from cytosine as termination signals for DNA synthesis. Sagher, D., Strauss, B. Nucleic Acids Res. (1985) [Pubmed]
  23. 5-Hydroxypyrimidine deoxynucleoside triphosphates are more efficiently incorporated into DNA by exonuclease-free Klenow fragment than 8-oxopurine deoxynucleoside triphosphates. Purmal, A.A., Kow, Y.W., Wallace, S.S. Nucleic Acids Res. (1994) [Pubmed]
  24. Effect of recA protein on the DNAse activities of the recBC enzyme. Prell, A., Wackernagel, W. J. Biol. Chem. (1981) [Pubmed]
  25. Site-specific frame-shift mutagenesis by the 1-nitropyrene-DNA adduct N-(deoxyguanosin-8-y1)-1-aminopyrene located in the (CG)3 sequence: effects of SOS, proofreading, and mismatch repair. Malia, S.A., Vyas, R.R., Basu, A.K. Biochemistry (1996) [Pubmed]
  26. The mechanism of recA polA lethality: suppression by RecA-independent recombination repair activated by the lexA(Def) mutation in Escherichia coli. Cao, Y., Kogoma, T. Genetics (1995) [Pubmed]
  27. Escherichia coli DNA polymerase III epsilon subunit increases Moloney murine leukemia virus reverse transcriptase fidelity and accuracy of RT-PCR procedures. Arezi, B., Hogrefe, H.H. Anal. Biochem. (2007) [Pubmed]
  28. Improvement of the 3'-5' exonuclease activity of Taq DNA polymerase by protein engineering in the active site. Park, Y., Choi, H., Lee, D.S., Kim, Y. Mol. Cells (1997) [Pubmed]
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