Conformational Dynamics of Human AP Endonuclease in Base Excision and Nucleotide Incision Repair Pathways

APEI is a multifunctional enzyme that plays a central role in base excision repair (BER) of DNA. APEI is also involved in the alternative nucleotide incision repair (NIR) pathway. We present an analysis of conformational dynamics and kinetic mechanisms of the full-length APEI and truncated N Delta 61-APEI lacking the N-terminal 61 amino acids (REFI domain) in BER and NIR pathways. The action of both enzyme forms were described by identical kinetic schemes. containing four stages corresponding to formation of the initial enzymesubstrate complex and isomerization of this complex; when a damaged substrate was present, these stages were followed by an irreversible catalytic stage resulting in the formation of the enzyme-product complex and the equilibrium stage of product release. For the first time we showed, that upon binding AP-containing DNA, the APEI structure underwent conformational changes before the chemical cleavage step. Under BER conditions, the REFI domain of APE I influenced the stability of both the enzyme-substrate and enzyme-product complexes, as well as the isomerization rate, but did not affect the rates of initial complex formation or catalysis. Under NIR conditions, the REFI domain affected both the rate of formation and the stability of the initial complex. In comparison with the full-length protein, N Delta 61-APEI did not display a decrease in NIR activity with a dihydrouracil-containing substrate. BER conditions decrease the rate of catalysis and strongly inhibit the rate of isomerization step for the NIR substrates. Under NIR conditions AP-endonuclease activity is still very efficient.