Crystallization and preliminary X-ray analysis of human endonuclease 1 (APE1) in complex with an oligonucleotide containing a 5,6-dihydrouracil (DHU) or an alpha-anomeric 2'-deoxyadenosine (alphadA) 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 alpha-anomeric 2'-deoxyadenosine (alphadA).T base pair. Diffraction data sets were collected to 2.2 and 2.7 A resolution from DNA-DHU-APE1 and DNA-alphadA-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.
Retailleau
Pascal
P
Laboratoire d'Enzymologie et de Biochimie Structurales, CNRS, F-91198 Gif-sur-Yvette Cedex, France.
Ishchenko
Alexander A
AA
Kuznetsov
Nikita A
NA
Saparbaev
Murat
M
Moréra
Solange
S
D003460:Crystallization; D018360:Crystallography, X-Ray; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase / Q000737:chemistry*; D003839:Deoxyadenosines / Q000737:chemistry*; D006801:Humans; D009841:Oligonucleotides / Q000737:chemistry*; D014498:Uracil / Q000737:chemistry
D003839:Deoxyadenosines; D009841:Oligonucleotides; D014498:Uracil; C085108:APEX1 protein, human; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase