Effects of mono- and divalent metal ions on DNA binding and catalysis of human apurinic/apyrimidinic endonuclease 1

Mol Biosyst. 2016 May 26;12(5):1527-39. doi: 10.1039/c6mb00128a. Epub 2016 Apr 11.


Here, we used stopped-flow fluorescence techniques to conduct a comparative kinetic analysis of the conformational transitions in human apurinic/apyrimidinic endonuclease 1 (APE1) and in DNA containing an abasic site in the course of their interaction. Effects of monovalent (K(+)) and divalent (Mg(2+), Mn(2+), Ca(2+), Zn(2+), Cu(2+), and Ni(2+)) metal ions on DNA binding and catalytic stages were studied. It was shown that the first step of substrate binding (corresponding to formation of a primary enzyme-substrate complex) does not depend on the concentration (0.05-5.0 mM) or the nature of divalent metal ions. In contrast, the initial DNA binding efficiency significantly decreased at a high concentration (5-250 mM) of monovalent K(+) ions, indicating the involvement of electrostatic interactions in this stage. It was also shown that Cu(2+) ions abrogated the DNA binding ability of APE1, possibly, due to a strong interaction with DNA bases and the sugar-phosphate backbone. In the case of Ca(2+) ions, the catalytic activity of APE1 was lost completely with retention of binding potential. Thus, the enzymatic activity of APE1 is increased in the order Zn(2+) < Ni(2+) < Mn(2+) < Mg(2+). Circular dichroism spectra and calculation of the contact area between APE1 and DNA reveal that Mg(2+) ions stabilize the protein structure and the enzyme-substrate complex.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Apoproteins / metabolism
  • Biocatalysis / drug effects*
  • Cations, Divalent / pharmacology*
  • Cations, Monovalent / pharmacology*
  • Circular Dichroism
  • DNA / chemistry
  • DNA / metabolism*
  • DNA-(Apurinic or Apyrimidinic Site) Lyase / chemistry
  • DNA-(Apurinic or Apyrimidinic Site) Lyase / metabolism*
  • Enzyme Activation / drug effects
  • Fluorescence Resonance Energy Transfer
  • Humans
  • Kinetics
  • Magnesium / pharmacology
  • Models, Molecular
  • Potassium / pharmacology
  • Substrate Specificity / drug effects


  • Apoproteins
  • Cations, Divalent
  • Cations, Monovalent
  • DNA
  • APEX1 protein, human
  • DNA-(Apurinic or Apyrimidinic Site) Lyase
  • Magnesium
  • Potassium