Crystallization and crystallographic characterization of the iron-sulfur-containing DNA-repair enzyme endonuclease III from Escherichia coli

Endonuclease III from Escherichia coli is an iron-sulfur enzyme possessing both DNA N-glycosylase and apurinic/apyrimidinic lyase activities. It could serve to repair damaged thymine residues in DNA via base excision-repair. We have crystallized endonuclease III by a combination of dialysis and seeding techniques after exploration of a wide variety of precipitants which failed to yield macroscopic crystals. Important features of the optimized crystallization include: the use of 5 to 10% glycerol, a temperature of 15°C, controlled dialysis to decrease ionic strength and macroseeding using a 200 mm-NaCl transfer buffer to dissolve microcrystalline contamination. The crystals belong to space group P2₁2₁2₁ with unit cell dimensions of a = 48·5 A ̊, b = 65·8 A ̊, c = 86·8 A ̊, α = β = γ = 90 °, have one 23 kDa monomer per asymmetric unit, and diffract to 1·84 Å. A native anomalous Patterson map located the iron-sulfur cluster and reaffirmed its existence. The reported crystallization procedures ensure an ample supply of crystals for the extensive heavy-atom derivative search necessary for this labile iron-sulfur enzyme. The elucidation of endonuclease III structure will facilitate not only the understanding of glycosylase and lyase mechanisms but also the structure and function of this new class of iron-sulfur proteins.