Co-crystallization of Staphylococcus aureus peptide deformylase (PDF) with potent inhibitors.

In bacteria the biosynthesis of all nascent polypeptides begins with N-formylmethionine. The post-translational removal of the N-formyl group is carried out by peptide deformylase (PDF). Processing of the N-formyl group from critical bacterial proteins is required for cell survival. This formylation/deformylation cycle is unique to eubacteria and is not utilized in eucaryotic cytosolic protein biosynthesis. Thus, inhibition of PDF would halt bacterial growth, spare host cell-function, and would be a novel mechanism for a new class of antibiotic. Diffraction-quality Se-met crystals of S. aureus PDF were prepared that belong to space group C222(1) with unit cell parameters of a = 94.1 b = 121.9 c = 47.6 A. Multiple anomalous dispersion data were collected at the Advanced Photon Source 17-ID beamline and used to solve the PDF structure to 1.9 A resolution. Crystals were also prepared with three PDF inhibitors: thiorphan, actinonin and PNU-172550. The thiorphan and actinonin co-crystals belong to space group C222(1) with similar unit-cell dimensions. Repeated attempts to generate a complex structure of PDF with PNU-172550 from the orthorhombic space group were unsuccessful. Crystallization screening identified an alternate C2 crystal form with unit-cell dimensions of a = 93.4 b = 42.5 c = 104.1 A, beta = 93 degrees.

Crystal structure of type II peptide deformylase from Staphylococcus aureus.

The first crystal structure of Class II peptide deformylase has been determined. The enzyme from Staphylococcus aureus has been overexpressed and purified in Escherichia coli and the structure determined by x-ray crystallography to 1.9 A resolution. The purified iron-enriched form of S. aureus peptide deformylase enzyme retained high activity over many months. In contrast, the iron-enriched form of the E. coli enzyme is very labile. Comparison of the two structures details many differences; however, there is no structural explanation for the dramatic activity differences we observed. The protein structure of the S. aureus enzyme reveals a fold similar, but not identical to, the well characterized E. coli enzyme. The most striking deviation of the S. aureus from the E. coli structure is the unique conformation of the C-terminal amino acids. The distinctive C-terminal helix of the latter is replaced by a strand in S. aureus which wraps around the enzyme, terminating near the active site. Although there are no differences at the amino acid level near the active site metal ion, significant changes are noted in the peptide binding cleft which may play a role in the design of general peptide deformylase inhibitors.

The essential role of a free sulfhydryl group in blocking the cholesteryl site of cholesteryl ester transfer protein (CETP).

Cholesteryl ester transfer protein (CETP) has at least one unpaired sulfhydryl residue, which we have shown previously to be in or near the active site region. We investigated the location of this unpaired cysteine residue(s) of CETP using chemical modification with fluorescent sulfhydryl-specific reagents, limited proteolysis, and amino acid/sequence analysis. The kinetics of labeling CETP by either 2-(4'-maleimidylanilino)-naphthalene-6-sulfonic acid (MIANS) or acrylodan were followed by observing the increase in fluorescence of the bound probes. Labeling was inhibited strongly by preincubation of the CETP with either PNU-617, a competitive inhibitor of cholesteryl ester (CE) transport, and TP2 antibody. In addition, the transfer activities of the substrate CE by the modified CETP's were also inhibited but not competitively. Finally, preincubation of the native protein with N-ethylmaleimide (NEM) resulted in inhibition of activity that was dependent upon the time of exposure of the protein to the alkylating agent. These results provide further evidence that there is a cysteine residue in the active site region of CETP and ligands that either react or bind to this residue produce steric hindrance to CE transfer activity. Finally, although not conclusive, results of the protein chemistry experiments with the modified CETP suggest that the cysteine residue at position 333 is unpaired.