Crystallization and preliminary X-ray analysis of human endonuclease 1 (APE1) in complex with an oligonucleotide containing a 5,6-dihydrouracil (DHU) or an α-anomeric 2′-deoxyadenosine (αdA) modified base

The multifunctional human apurinic/apyrimidinic (AP) endonuclease 1 (APE1) is a key enzyme involved in both the base-excision repair (BER) and nucleotide-incision repair (NIR) pathways. In the NIR pathway, APE1 incises DNA 5′ to a number of oxidatively damaged bases. APE1 was crystallized in the presence of a 15-mer DNA containing an oxidatively damaged base in a single central 5,6-­dihydrouracil (DHU)·T or α-anomeric 2′-deoxyadenosine (αdA)·T base pair. Diffraction data sets were collected to 2.2 and 2.7 Å resolution from DNA-DHU–APE1 and DNA-αdA–APE1 crystals, respectively. The crystals were isomorphous and contained one enzyme molecule in the asymmetric unit. Molecular replacement was performed and the initial electron-density maps revealed that in both complexes APE1 had crystallized with a degradation DNA product reduced to a 6-mer, suggesting that NIR and exonuclease reactions occurred prior to crystallization.