Crystallization and preliminary crystallographic analysis of endonuclease VIII in its uncomplexed form

• Published in: Acta crystallographica. Section D, Biological crystallography. Biological crystallography., 2004-08, Vol.60 (8), p.1476-1480
• Main Authors: Golan, Gali, Zharkov, Dmitry O., Fernandes, Andrea S., Zaika, Elena, Kycia, Jadwiga H., Wawrzak, Zdzislaw, Grollman, Arthur P., Shoham, Gil
• Format: Article
• Language: English
• Subjects: base excision; Crystallization; Crystallography, X-Ray; Deoxyribonuclease (Pyrimidine Dimer) - chemistry; Deoxyribonuclease (Pyrimidine Dimer) - genetics; Deoxyribonuclease (Pyrimidine Dimer) - metabolism; DNA repair; endonuclease VIII; Escherichia coli - enzymology; Escherichia coli - genetics; Escherichia coli Proteins - chemistry; Escherichia coli Proteins - genetics; Escherichia coli Proteins - metabolism; mutagenesis; Mutation - genetics; Nei; oxidative damage
• ISSN: 1399-0047; 0907-4449; 1399-0047
• DOI: 10.1107/S0907444904013241

The Escherichia coli DNA repair enzyme endonuclease VIII (EndoVIII or Nei) excises oxidized pyrimidines from damaged DNA substrates. It overlaps in substrate specificity with endonuclease III and may serve as a back‐up for this enzyme in E. coli. The three‐dimensional structure of Nei covalently complexed with DNA has been recently determined, revealing the critical amino‐acid residues required for DNA binding and catalytic activity. Based on this information, several site‐specific mutants of the enzyme have been tested for activity against various substrates. Although the crystal structure of the DNA‐bound enzyme has been fully determined, the important structure of the free enzyme has not previously been analyzed. In this report, the crystallization and preliminary crystallographic characterization of DNA‐free Nei are described. Four different crystal habits are reported for wild‐type Nei and two of its catalytic mutants. Despite being crystallized under different conditions, all habits belong to the same crystal form, with the same space group (I222) and a similar crystallographic unit cell (average parameters a = 57.7, b = 80.2, c = 169.7 Å). Two of these crystal habits, I and IV, appear to be suitable for full crystallographic analysis. Crystal habit I was obtained by vapour diffusion using PEG 8000, glycerol and calcium acetate. Crystal habit IV was obtained by a similar method using PEG 400 and magnesium chloride. Both crystals are mechanically strong and stable in the X‐ray beam once frozen under cold nitrogen gas. A full diffraction data set has recently been collected from a wild‐type Nei crystal of habit I (2.6 Å resolution, 85.2% completeness, Rmerge = 9.8%). Additional diffraction data were collected from an Nei‐R252A crystal of habit IV (2.05 Å resolution, 99.9% completeness, Rmerge = 6.0%) and an Nei‐E2A crystal of habit IV (2.25 Å resolution, 91.7% completeness, Rmerge = 6.2%). These diffraction data were collected at 95–100 K using a synchrotron X‐ray source and a CCD area detector. All three data sets are currently being used to obtain crystallographic phasing via molecular‐replacement techniques.