Crystal structure and mutational analysis of human uracil-DNA glycosylase: structural basis for specificity and catalysis

Cell. 1995 Mar 24;80(6):869-78. doi: 10.1016/0092-8674(95)90290-2.


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Asparagine
  • Binding Sites
  • Catalysis
  • Cloning, Molecular
  • Crystallography, X-Ray / methods
  • DNA Damage
  • DNA Glycosylases*
  • DNA Mutational Analysis
  • DNA Repair
  • Escherichia coli
  • Histidine
  • Humans
  • Hydrogen Bonding
  • Models, Molecular
  • Molecular Sequence Data
  • N-Glycosyl Hydrolases / biosynthesis
  • N-Glycosyl Hydrolases / chemistry*
  • N-Glycosyl Hydrolases / metabolism*
  • Protein Biosynthesis
  • Protein Conformation*
  • Protein Folding*
  • Protein Structure, Secondary
  • Rabbits
  • Recombinant Proteins / biosynthesis
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / metabolism
  • Reticulocytes / metabolism
  • Substrate Specificity
  • Uracil-DNA Glycosidase


  • Recombinant Proteins
  • Histidine
  • Asparagine
  • DNA Glycosylases
  • N-Glycosyl Hydrolases
  • Uracil-DNA Glycosidase