Three-dimensional structural model analysis of the binding site of lithocholic acid, an inhibitor of DNA polymerase beta and DNA topoisomerase II

J Biochem. 2001 Nov;130(5):657-64. doi: 10.1093/oxfordjournals.jbchem.a003031.


The molecular action of lithocholic acid (LCA), a selective inhibitor of mammalian DNA polymerase beta (pol beta), was investigated. We found that LCA could also strongly inhibit the activity of human DNA topoisomerase II (topo II). No other DNA metabolic enzymes tested were affected by LCA. Therefore, LCA should be classified as an inhibitor of both pol beta and topo II. Here, we report the molecular interaction of LCA with pol beta and topo II. By three-dimensional structural model analysis and by comparison with the spatial positioning of specific amino acids binding to LCA on pol beta (Lys60, Leu77, and Thr79), we obtained supplementary information that allowed us to build a structural model of topo II. Modeling analysis revealed that the LCA-interaction interface in both enzymes has a pocket comprised of three amino acids in common, which binds to the LCA molecule. In topo II, the three amino acid residues were Lys720, Leu760, and Thr791. These results suggested that the LCA binding domains of pol beta and topo II are three-dimensionally very similar.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • African Swine Fever Virus / enzymology
  • Amino Acid Sequence
  • Animals
  • Binding Sites
  • Cattle
  • Cricetinae
  • DNA / metabolism
  • DNA Polymerase beta / antagonists & inhibitors
  • DNA Polymerase beta / chemistry*
  • DNA Polymerase beta / metabolism
  • DNA Topoisomerases, Type II / chemistry*
  • DNA Topoisomerases, Type II / metabolism
  • Drosophila / enzymology
  • Enzyme Inhibitors / chemistry
  • Enzyme Inhibitors / pharmacology
  • Evolution, Molecular
  • Humans
  • Inhibitory Concentration 50
  • Leucine / metabolism
  • Lithocholic Acid / chemistry*
  • Lithocholic Acid / pharmacology
  • Lysine / metabolism
  • Mice
  • Models, Chemical
  • Molecular Mimicry
  • Molecular Sequence Data
  • Molecular Weight
  • Protein Structure, Tertiary
  • Rats
  • Sequence Homology, Amino Acid
  • Threonine / metabolism
  • Yeasts / enzymology


  • Enzyme Inhibitors
  • Threonine
  • Lithocholic Acid
  • DNA
  • DNA Polymerase beta
  • DNA Topoisomerases, Type II
  • Leucine
  • Lysine