Chinese hamster AP endonuclease operates by a two-metal ion assisted catalytic mechanism

The APE1, an important mammalian AP endonuclease, is an essential enzyme in the base excision DNA repair pathway (BER). The number of metal ions involved directly in the catalysis remains controversial. Here we describe the metal ion titration experiments that demonstrate the requirement for two metal ions for the endonuclease activity of the Chinese hamster APE1. The titration with the non-activating metal ion La3+ showed a biphasic behavior with activating and inhibitory effects of La3+ in the range of 0–100 μM in the presence of 5 mM Mg2+. Modeling of the enzyme-substrate/product complexes provided insight into the endonuclease activity and elucidated the nature of the crystal structures. Accordingly, we proposed a reaction scheme for the two-metal ion assisted catalysis of chAPE1 endonuclease activity.

► Kinetic evaluation of chAPE1 metal ion specificity.
► Use of inhibitory and activating metal ion to probe for the catalytic mechanism.
► Two metal ion assisted catalysis describes best the mechanism of chAPE1.
► Crystal structures depict non-productive metal ion complexes with substrates and products.