Human apurinic/apyrimidinic endonuclease 1

Abstract

Significance: Human apurinic/apyrimidinic endonuclease 1 (APE1, also known as REF-1) was isolated based on its ability to cleave at AP sites in DNA or activate the DNA binding activity of certain transcription factors. We review herein topics related to this multi-functional DNA repair and stress-response protein.

Recent advances: APE1 displays homology to Escherichia coli exonuclease III and is a member of the divalent metal-dependent α/β fold-containing phosphoesterase superfamily of enzymes. APE1 has acquired distinct active site and loop elements that dictate substrate selectivity, and a unique N-terminus which at minimum imparts nuclear targeting and interaction specificity. Additional activities ascribed to APE1 include 3'-5' exonuclease, 3'-repair diesterase, nucleotide incision repair, damaged or site-specific RNA cleavage, and multiple transcription regulatory roles.

Critical issues: APE1 is essential for mouse embryogenesis and contributes to cell viability in a genetic background-dependent manner. Haploinsufficient APE1(+/-) mice exhibit reduced survival, increased cancer formation, and cellular/tissue hyper-sensitivity to oxidative stress, supporting the notion that impaired APE1 function associates with disease susceptibility. Although abnormal APE1 expression/localization has been seen in cancer and neuropathologies, and impaired-function variants have been described, a causal link between an APE1 defect and human disease remains elusive.

Future directions: Ongoing efforts aim at delineating the biological role(s) of the different APE1 activities, as well as the regulatory mechanisms for its intra-cellular distribution and participation in diverse molecular pathways. The determination of whether APE1 defects contribute to human disease, particularly pathologies that involve oxidative stress, and whether APE1 small-molecule regulators have clinical utility, is central to future investigations.

FIG. 1.

Chemical structure of a hydrolytic abasic site and the cleavage position for the major classes of AP site incision enzymes. The phosphodiester bond cleavage site, immediately adjacent to an abasic lesion (see arrows), is shown for a class I AP lyase (site B) and a class II AP endonuclease (site A). Class I AP lyases cleave via β-elimination, generating a 3′-α,β-unsaturated aldehyde and a 5′-phosphate. Class II AP endonucleases, for example, APE1, incise the DNA backbone hydrolytically, leaving behind 5′-deoxyribose phosphate and 3′-hydroxyl termini. For simplicity, just the strand containing the AP site is shown, with two “random” flanking bases. Images were created using the Accelrys Draw 4.1 software (Accelrys, San Diego, CA). AP, apurinic/apyrimidinic; APE1, apurinic/apyrimidinic endonuclease 1.

FIG. 2.

Schematic of key elements in the human APE1 protein. The nuclease domain of APE1 spans roughly residues 64 to 318, with the N-terminal portion of the protein encompassing much of the transcriptional regulatory functions of APE1 (with some overlap between the two regions). Key active site residues for the nuclease activities of APE1 (i.e., E96, D210, and H309) are identified via underline, and several PTM sites are depicted. A recently identified, lysine-rich, rRNA binding site is also designated. See text for further details. NLS, nuclear localization signal; NES, nuclear export signal; MTS, mitochondrial targeting sequence; PTM, post-translational modification.

FIG. 3.

Human APE1 orthologs and key protein structural elements. (A) APE1 orthologs. The particular species (left) and gene name (right) are indicated. Shown is the primary structure, with the AP endonuclease domain designated as a green box. Total amino-acid sequence length and percent similarity with human APE1 are specified. SAP, SAF-A/B, Acinus and PIAS motif, which is a putative DNA/RNA binding domain; EEP, Exonuclease-Endonuclease-Phosphatase domain; ZF, zinc finger. (B) APE1 structural features. All images were created using the DS ViewerPro software (Accelrys, San Diego, CA). Left: ribbon diagram of human APE1 [coordinates from 1BIX (63)]. The major recognition loops are designated. Middle: diagram of APE1 bound to un-incised AP-DNA [coordinates from 1DE8 (145)]. Recognition loops are indicated, and the abasic site is circled. Note the 35° kinking of the DNA backbone (emphasized by arrow). Right: diagram of the binding surface and active site of APE1 in complex with incised AP-DNA and Mn²⁺ [coordinates from 1DE9 (145)]. DNA strands are shown in white, with the 5′-abasic residue designated in yellow. The protein is shown as a cyan ribbon. The recognition pocket (comprising F266, W280, and L282) and several key active site residues (E96, D210, and H309) are highlighted. The recognition loops, and two key binding residues (R177 and M270), are also indicated. The catalytic metal ion is depicted as a purple sphere. To see this illustration in color, the reader is referred to the web version of this article at www.liebertpub.com/ars

FIG. 4.

The APE1 galaxy. As highlighted within, APE1 has multiple biochemical activities that impart multiple biological roles. These functions affect various cellular processes that can ultimately impact disease susceptibility, therapeutic response, and prognosis. In addition, complex mechanisms that involve protein interactions and PTMs regulate not only the activities of APE1, but also its intra-cellular compartmentalization. See text for details. To see this illustration in color, the reader is referred to the web version of this article at www.liebertpub.com/ars