Crystallization and preliminary X-ray crystallographic analysis of peptide deformylase (PDF) from Bacillus cereus in ligand-free and actinonin-bound forms

Abstract

In bacteria, protein expression initiates with an N-formyl group and this needs to be removed in order to ensure proper bacterial growth. These formylation and deformylation processes are unique to eubacteria; therefore, inhibition of these would provide a novel antibacterial therapy. Deformylation is carried out by peptide deformylase (PDF). PDF from Bacillus cereus, one of the major pathogenic bacteria, was cloned into expression plasmid pET-28a (Novagen), overexpressed in Escherichia coli BL21 (DE3) and purified to high quality. Crystals have been obtained of both ligand-free PDF and PDF to which actinonin, a highly potent naturally occurring inhibitor, is bound. Both crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 42.72, b = 44.04, c = 85.19 A and a = 41.31, b = 44.56, c = 84.47 A, respectively. Diffraction data were collected to 1.7 A resolution for the inhibitor-free crystals and to 2.0 A resolution for the actinonin-bound crystals.

Figure 1

(a) A crystal of B. cereus peptide deformylase. Its approximate dimensions are 0.2 × 0.2 × 0.6 mm. (b) A crystal of B. cereus peptide deformylase grown in the presence of actinonin, with approximate dimensions 0.4 × 0.2 × 0.4 mm.