Substrate discrimination by formamidopyrimidine-DNA glycosylase. A mutational analysis

Elena I. Zaika, Rebecca A. Perlow, Eileen Matz, Suse Broyde, Rotem Gilboa, Arthur P. Grollman, Dmitry O. Zharkov

Research output: Contribution to journalArticle

Abstract

Formamidopyrimidine-DNA glycosylase (Fpg) is a primary participant in the repair of 8-oxoguanine, an abundant oxidative DNA lesion. Although the structure of Fpg has been established, amino acid residues that define damage recognition have not been identified. We have combined molecular dynamics and bioinformatics approaches to address this issue. Site-specific mutagenesis coupled with enzyme kinetics was used to test our predictions. On the basis of molecular dynamics simulations, Lys-217 was predicted to interact with the O8 of extrahelical 8-oxoguanine accommodated in the binding pocket. Consistent with our computational studies, mutation of Lys-217 selectively reduced the ability of Fpg to excise 8-oxoguanine from DNA. Dihydrouracil, also a substrate for Fpg, served as a nonspecific control. Other residues involved in damage recognition (His-89, Arg-108, and Arg-109) were identified by combined conservation/structure analysis. Arg-108, which forms two hydrogen bonds with cytosine in Fpg-DNA, is a major determinant of opposite-base specificity. Mutation of this residue reduced excision of 8-oxoguanine from thermally unstable mispairs with guanine or thymine, while excision from the stable cytosine and adenine base pairs was less affected. Mutation of His-89 selectively diminished the rate of excision of 8-oxoguanine, whereas mutation of Arg-109 nearly abolished binding of Fpg to damaged DNA. Taken together, these results suggest that His-89 and Arg-109 form part of a reading head, a structural feature used by the enzyme to scan DNA for damage. His-89 and Lys-217 help determine the specificity of Fpg in recognizing the oxidatively damaged base, while Arg-108 provides specificity for bases positioned opposite the lesion.

Original languageEnglish (US)
Pages (from-to)4849-4861
Number of pages13
JournalJournal of Biological Chemistry
Volume279
Issue number6
DOIs
StatePublished - Feb 6 2004

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DNA-Formamidopyrimidine Glycosylase
Substrates
DNA
Mutation
Cytosine
Molecular Dynamics Simulation
Molecular dynamics
Enzyme kinetics
Mutagenesis
Thymine
Guanine
Adenine
Enzymes
Bioinformatics
Site-Directed Mutagenesis
Computational Biology
Base Pairing
DNA Damage
Reading
Hydrogen

ASJC Scopus subject areas

  • Biochemistry

Cite this

Zaika, E. I., Perlow, R. A., Matz, E., Broyde, S., Gilboa, R., Grollman, A. P., & Zharkov, D. O. (2004). Substrate discrimination by formamidopyrimidine-DNA glycosylase. A mutational analysis. Journal of Biological Chemistry, 279(6), 4849-4861. https://doi.org/10.1074/jbc.M310262200

Substrate discrimination by formamidopyrimidine-DNA glycosylase. A mutational analysis. / Zaika, Elena I.; Perlow, Rebecca A.; Matz, Eileen; Broyde, Suse; Gilboa, Rotem; Grollman, Arthur P.; Zharkov, Dmitry O.

In: Journal of Biological Chemistry, Vol. 279, No. 6, 06.02.2004, p. 4849-4861.

Research output: Contribution to journalArticle

Zaika, EI, Perlow, RA, Matz, E, Broyde, S, Gilboa, R, Grollman, AP & Zharkov, DO 2004, 'Substrate discrimination by formamidopyrimidine-DNA glycosylase. A mutational analysis', Journal of Biological Chemistry, vol. 279, no. 6, pp. 4849-4861. https://doi.org/10.1074/jbc.M310262200
Zaika, Elena I. ; Perlow, Rebecca A. ; Matz, Eileen ; Broyde, Suse ; Gilboa, Rotem ; Grollman, Arthur P. ; Zharkov, Dmitry O. / Substrate discrimination by formamidopyrimidine-DNA glycosylase. A mutational analysis. In: Journal of Biological Chemistry. 2004 ; Vol. 279, No. 6. pp. 4849-4861.
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