Crystal structure of a human alkylbase-DNA repair enzyme complexed to DNA: mechanisms for nucleotide flipping and base excision.
DNA N-glycosylases are base excision-repair proteins that locate and cleave damaged bases from DNA as the first step in restoring the genetic blueprint. The human enzyme 3-methyladenine DNA glycosylase removes a diverse group of damaged bases from DNA, including cytotoxic and mutagenic alkylation adducts of purines. We report the crystal structure of human 3-methyladenine DNA glycosylase complexed to a mechanism-based pyrrolidine inhibitor. The enzyme has intercalated into the minor groove of DNA, causing the abasic pyrrolidine nucleotide to flip into the enzyme active site, where a bound water is poised for nucleophilic attack. The structure shows an elegant means of exposing a nucleotide for base excision as well as a network of residues that could catalyze the in-line displacement of a damaged base from the phosphodeoxyribose backbone.
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Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA.
Schärer
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Samson
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Verdine
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Ellenberger
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D000478:Alkylation; D020134:Catalytic Domain; D003461:Crystallography; D004247:DNA / Q000378:metabolism*; D045647:DNA Glycosylases; D011088:DNA Ligases / Q000737:chemistry*; D004268:DNA-Binding Proteins / Q000737:chemistry; D006031:Glycosylation; D006801:Humans; D008969:Molecular Sequence Data; D009699:N-Glycosyl Hydrolases / Q000737:chemistry*; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid; D014867:Water / Q000737:chemistry
D004268:DNA-Binding Proteins; D009711:Nucleotides; D014867:Water; D004247:DNA; C021565:3-methyladenine-DNA glycosylase; D045647:DNA Glycosylases; D009699:N-Glycosyl Hydrolases; D011088:DNA Ligases