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. Author manuscript; available in PMC: 2015 Dec 11.
Published in final edited form as: Biochemistry. 2010 Aug 3;49(30):6451–6461. doi: 10.1021/bi100769k

Scheme 1.

Scheme 1

Kinetic Scheme for the APE1 Interaction with AP-, F-, and G-Containing DNAa

aE, APE1; S, free DNA substrate; (ES), bimolecular encounter complex; (ES)′ and (ES)″, subsequent states of the APE1-DNA complex; (EP), complex of APE1 with the DNA product; P, product of the substrate incision. Constants k1, k2, and k3 characterize the forward direction, whereas k−1, k−2, and k−3 are the rate constants for the reverse reactions; kirr corresponds to the irreversible chemical step. Kd is an equilibrium constant calculated as the k4/k−4 ratio. In the case of F-substrate cleavage, an additional stage of the mechanism is shown in red. AP, AP-substrate; F, F-substrate; G, G-ligand.