Purification, crystallization and preliminary structural analysis of nucleoside diphosphate kinase from Bacillus anthracis

Abstract

Bacillus anthracis nucleoside diphosphate kinase (BaNdk) is an enzyme whose primary function is to maintain deoxynucleotide triphosphate (dNTP) pools by converting deoxynucleotide diphosphates to triphosphates using ATP as the major phosphate donor. Although the structures of Ndks from a variety of organisms have been elucidated, the enzyme from sporulating bacteria has not been structurally characterized to date. Crystals of the B. anthracis enzyme were grown using the vapour-diffusion method from a hanging drop consisting of 2 microl 10 mg ml(-1) protein in 50 mM Tris-HCl pH 8.0, 50 mM NaCl, 5 mM EDTA equilibrated against 500 microl reservoir solution consisting of 2.25 M ammonium formate and 0.1 M HEPES buffer pH 7.25. Diffraction data extending to 2.0 A were collected at room temperature from a single crystal with unit-cell parameters a = b = 107.53, c = 52.3 A. The crystals are hexagonal in shape and belong to space group P6(3)22. The crystals contain a monomer in the asymmetric unit, which corresponds to a Matthews coefficient (V(M)) of 2.1 A(3) Da(-1) and a solvent content of about 36.9%.

Figure 1

Crystal of B. anthracis nucleoside diphosphate kinase.

Figure 2

Packing of molecules in the crystal structure of B. anthracis Ndk. The association of the hexamer as a dimer of trimers is clearly visible.