Structure of Formamidopyrimidine-DNA Glycosylase Covalently Complexed to DNA

Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. The Schiff base intermediate formed during this reaction between Escherichia coli Fpg and DNA was trapped by reduction with sodium borohydride, and the structure of the resulting covalent...

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Bibliographic Details
Published in:The Journal of biological chemistry 2002-05, Vol.277 (22), p.19811-19816
Main Authors: Gilboa, Rotem, Zharkov, Dmitry O., Golan, Gali, Fernandes, Andrea S., Gerchman, Sue Ellen, Matz, Eileen, Kycia, Jadwiga H., Grollman, Arthur P., Shoham, Gil
Format: Article
Language:English
Subjects:
Arginine - chemistry
Asparagine - chemistry
Binding Sites
Catalytic Domain
Crystallography, X-Ray
DNA - chemistry
DNA-Formamidopyrimidine Glycosylase
Electrons
Escherichia coli
Escherichia coli - enzymology
Escherichia coli Proteins
formamidopyrimidine-DNA glycosylase
Fpg protein
Histidine - chemistry
Hydrogen Bonding
Lysine - chemistry
Methionine - chemistry
Models, Molecular
Mutation
N-Glycosyl Hydrolases - chemistry
Nucleic Acid Conformation
Oligonucleotides - chemistry
Phenylalanine - chemistry
Protein Binding
Static Electricity
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Summary:Formamidopyrimidine-DNA glycosylase (Fpg) is a DNA repair enzyme that excises oxidized purines from damaged DNA. The Schiff base intermediate formed during this reaction between Escherichia coli Fpg and DNA was trapped by reduction with sodium borohydride, and the structure of the resulting covalently cross-linked complex was determined at a 2.1-Å resolution. Fpg is a bilobal protein with a wide, positively charged DNA-binding groove. It possesses a conserved zinc finger and a helix-two turn-helix motif that participate in DNA binding. The absolutely conserved residues Lys-56, His-70, Asn-168, and Arg-258 form hydrogen bonds to the phosphodiester backbone of DNA, which is sharply kinked at the lesion site. Residues Met-73, Arg-109, and Phe-110 are inserted into the DNA helix, filling the void created by nucleotide eversion. A deep hydrophobic pocket in the active site is positioned to accommodate an everted base. Structural analysis of the Fpg-DNA complex reveals essential features of damage recognition and the catalytic mechanism of Fpg.
ISSN:0021-9258
1083-351X
DOI:10.1074/jbc.M202058200