Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis.
Crystal structures of the DNA repair enzyme human uracil-DNA glycosylase (UDG), combined with mutational analysis, reveal the structural basis for the specificity of the enzyme. Within the classic alpha/beta fold of UDG, sequence-conserved residues form a positively charged, active-site groove the width of duplex DNA, at the C-terminal edge of the central four-stranded parallel beta sheet. In the UDG-6-aminouracil complex, uracil binds at the base of the groove within a rigid preformed pocket that confers selectivity for uracil over other bases by shape complementary and by main chain and Asn-204 side chain hydrogen bonds. Main chain nitrogen atoms are positioned to stabilize the oxyanion intermediate generated by His-268 acting via nucleophilic attack or general base mechanisms. Specific binding of uracil flipped out from a DNA duplex provides a structural mechanism for damaged base recognition.
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Department of Molecular Biology, Scripps Research Institute, La Jolla, California 92037.
Arvai
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Slupphaug
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Kavli
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Alseth
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Krokan
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D000595:Amino Acid Sequence; D000818:Animals; D001216:Asparagine; D001665:Binding Sites; D002384:Catalysis; D003001:Cloning, Molecular; D018360:Crystallography, X-Ray / Q000379:methods; D004249:DNA Damage; D045647:DNA Glycosylases; D004252:DNA Mutational Analysis; D004260:DNA Repair; D004926:Escherichia coli; D006639:Histidine; D006801:Humans; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009699:N-Glycosyl Hydrolases / Q000096:biosynthesis / Q000737:chemistry* / Q000378:metabolism*; D014176:Protein Biosynthesis; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011817:Rabbits; D011994:Recombinant Proteins / Q000096:biosynthesis / Q000737:chemistry / Q000378:metabolism; D012156:Reticulocytes / Q000378:metabolism; D013379:Substrate Specificity; D051981:Uracil-DNA Glycosidase
D011994:Recombinant Proteins; D006639:Histidine; D001216:Asparagine; D045647:DNA Glycosylases; D009699:N-Glycosyl Hydrolases; D051981:Uracil-DNA Glycosidase