Mechanisms of base selection by the Escherichia coli mispaired uracil glycosylase

Pingfang Liu, Jacob A. Theruvathu, Agus Darwanto, Victoria Valinluck Lao, Tod Pascal, William Goddard, Lawrence Sowers

Research output: Contribution to journalArticle

14 Citations (Scopus)

Abstract

The repair of the multitude of single-base lesions formed daily in cells of all living organisms is accomplished primarily by the base excision repair pathway that initiates repair through a series of lesion-selective glycosylases. In this article, single-turnover kinetics have been measured on a series of oligonucleotide substrates containing both uracil and purine analogs for the Escherichia coli mispaired uracil glycosylase (MUG). The relative rates of glycosylase cleavage have been correlated with the free energy of helix formation and with the size and electronic inductive properties of a series of uracil 5-substituents. Data are presented that MUG can exploit the reduced thermodynamic stability of mispairs to distinguish U:A from U:G pairs. Discrimination against the removal of thymine results primarily from the electron-donating property of the thymine 5-methyl substituent, whereas the size of the methyl group relative to a hydrogen atom is a secondary factor. A series of parameters have been obtained that allow prediction of relative MUG cleavage rates that correlate well with observed relative rates that vary over 5 orders of magnitude for the series of base analogs examined. We propose that these parameters may be common among DNA glycosylases; however, specific glycosylases may focus more or less on each of the parameters identified. The presence of a series of glycosylases that focus on different lesion properties, all coexisting within the same cell, would provide a robust and partially redundant repair system necessary for the maintenance of the genome.

Original languageEnglish (US)
Pages (from-to)8829-8836
Number of pages8
JournalJournal of Biological Chemistry
Volume283
Issue number14
DOIs
StatePublished - Apr 4 2008
Externally publishedYes

Fingerprint

Uracil
Escherichia coli
Repair
Thymine
DNA Glycosylases
Thermodynamics
Oligonucleotides
DNA Repair
Free energy
Hydrogen
Thermodynamic stability
Genes
Maintenance
Genome
Electrons
Atoms
Kinetics
Substrates

ASJC Scopus subject areas

  • Biochemistry
  • Cell Biology
  • Molecular Biology

Cite this

Liu, P., Theruvathu, J. A., Darwanto, A., Lao, V. V., Pascal, T., Goddard, W., & Sowers, L. (2008). Mechanisms of base selection by the Escherichia coli mispaired uracil glycosylase. Journal of Biological Chemistry, 283(14), 8829-8836. https://doi.org/10.1074/jbc.M707174200

Mechanisms of base selection by the Escherichia coli mispaired uracil glycosylase. / Liu, Pingfang; Theruvathu, Jacob A.; Darwanto, Agus; Lao, Victoria Valinluck; Pascal, Tod; Goddard, William; Sowers, Lawrence.

In: Journal of Biological Chemistry, Vol. 283, No. 14, 04.04.2008, p. 8829-8836.

Research output: Contribution to journalArticle

Liu, P, Theruvathu, JA, Darwanto, A, Lao, VV, Pascal, T, Goddard, W & Sowers, L 2008, 'Mechanisms of base selection by the Escherichia coli mispaired uracil glycosylase', Journal of Biological Chemistry, vol. 283, no. 14, pp. 8829-8836. https://doi.org/10.1074/jbc.M707174200
Liu P, Theruvathu JA, Darwanto A, Lao VV, Pascal T, Goddard W et al. Mechanisms of base selection by the Escherichia coli mispaired uracil glycosylase. Journal of Biological Chemistry. 2008 Apr 4;283(14):8829-8836. https://doi.org/10.1074/jbc.M707174200
Liu, Pingfang ; Theruvathu, Jacob A. ; Darwanto, Agus ; Lao, Victoria Valinluck ; Pascal, Tod ; Goddard, William ; Sowers, Lawrence. / Mechanisms of base selection by the Escherichia coli mispaired uracil glycosylase. In: Journal of Biological Chemistry. 2008 ; Vol. 283, No. 14. pp. 8829-8836.
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