APE1: A skilled nucleic acid surgeon

Abstract

Before a deleterious DNA lesion can be replaced with its undamaged counterpart, the lesion must first be removed from the genome. This process of removing and replacing DNA lesions is accomplished by the careful coordination of several protein factors during DNA repair. One such factor is the multifunctional enzyme human apurinic/apyrimidinic endonuclease 1 (APE1), known best for its DNA backbone cleavage activity at AP sites during base excision repair (BER). APE1 preforms AP site incision with surgical precision and skill, by sculpting the DNA to place the cleavage site in an optimal position for nucleophilic attack within its compact protein active site. APE1, however, has demonstrated broad surgical expertise, and applies its DNA cleavage activity to a wide variety of DNA and RNA substrates. Here, we discuss what is known and unknown about APE1 cleavage mechanisms, focusing on structural and mechanistic considerations. Importantly, disruptions in the biological functions associated with APE1 are linked to numerous human maladies, including cancer and neurodegenerative diseases. The continued elucidation of APE1 mechanisms is required for rational drug design towards novel and strategic ways to target its associated repair pathways.

Keywords: AP sites; APE1; DNA cleavage; DNA damage; DNA repair; End processing; Nucleotide incision repair; RNA metabolism.

Fig. 1

Schematic of the BER pathway (black) showing the role of APE1 AP-endonuclease activity and APE1 exonuclease activity (blue) in proofreading 3ʹ mismatches and removing 3ʹ end damage. DNA damage and mismatches are highlighted in red.

Fig. 2

APE1 AP-endonuclease reaction. (A) The APE1 active site showing the nucleophilic water and key active site residues. (B) Surface representation of the APE1:AP-DNA complex demonstrating the flipped out AP site and compact active site. Protein is shown in cyan and DNA residues in gray.

Fig. 3

The APE1 exonuclease reaction of a 3′ mismatch. (A) Overview of exonuclease substrate complex. The site of cleavage is indicated by the arrow. The 3ʹ mismatched cytosine, its flanking base, and the opposing base are shown in stick format (gray carbons). (B) Focused view of the APE1 exonuclease active site showing key catalytic residues, cleavage site, and nucleophilic water with key interactions indicated by dashed lines. (C) Surface representation of exonuclease DNA substrate showing the bend of the DNA to accommodate the 3ʹ mismatched base. The protein is shown in green and the DNA in gray.

Fig. 4

Structures of several APE1 substrates demonstrating their diversity. Red lines indicate the site of APE1 cleavage.