Partial purification of Pdel from Saccharomyces cerevisiae: Enzymatic redundancy for the repair of 3'-terminal DNA lesions and abasic sites in yeast

Earlier work indicates that the major DNA repair phosphodiesterase (PDE) in yeast cells is the well-characterized Apnl protein. Apnl demonstrates both Mg²⁺-independent PDE activity and Mg²⁺-independent class II apurinic/apyrimidinic (AP) endonuclease activity and represents greater than 90% of the activity detected in crude extracts from wild-type yeast cells. Apn1 is related to Escherichia coli endonuclease IV, both in its enzymatic properties and its amino acid sequence. In this work, we report the partial purification of a novel yeast protein, Pde l, present in Apn1-deficient cells. Pde1 is purified by sequential BioRex-70, PBE118, and MonoS chromatography steps using a sensitive and highly specific 3'- phosphoglycolate-terminated oligonucleotide-based assay as a measure of PDE activity. Mg²⁺-stimulated PDE and Mg²⁺-stimulated class II AP endonuclease copurify during this procedure. These results indicate that yeast, like many other organisms studied to date, has enzymatic redundancy for the repair of 3'- blocking groups and abasic sites.