Schizosaccharomyces pombe Apn2p, which provides the major AP endonuclease activity of yeast cells, functions in an initial step of base excision repair (BER). Cells lacking Apn2p exhibit severe hypersensitivity to methylmethane sulfonate (MMS) treatment. N-terminal regions of S. pombe and Saccharomyces cerevisiae Apn2p and human APE2 proteins have homology to Escherichia coli exonuclease III and constitute a catalytic domain. The C-terminal regions of the Apn2/APE2-type enzymes contain a binding motif to proliferative cell nuclear antigen (PCNA) and a sequence homologous to the DNA topoisomerase III (TOP3) family. S. cerevisiae Apn2 and hAPE2 have been shown to physically interact with PCNA in vivo and in vitro. Moreover S. cerevisiae PCNA stimulates the 3′ to 5′ exonuclease and 3′-phosphodiesterase activities of Apn2p in vitro. Here, we describe the functions of the PCNA-binding motif and the TOP3 homologous region of S. pombe Apn2p in the repair of alkylation DNA damage. Apn2p with mutations in these conserved regions was exogenously expressed in apn2-disrupted cells and its ability to complement MMS sensitivity was measured. The results demonstrated that the PCNA-binding motif and the TOP3 region are dispensable for BER in S. pombe cells. This suggests that the C-terminal domains in the Apn2p/APE2-type enzymes differentially contribute to the BER pathway in yeast and mammalian cells.