The Crystal Structures of Four Peptide Deformylases Bound to the Antibiotic Actinonin Reveal Two Distinct Types: A Platform for the Structure-based Design of Antibacterial Agents

• Published in: Journal of molecular biology Vol. 320; no. 5; pp. 951 - 962
• Main Authors: Guilloteau, Jean-Pierre, Mathieu, Magali, Giglione, Carmela, Blanc, Véronique, Dupuy, Alain, Chevrier, Miline, Gil, Patricia, Famechon, Alain, Meinnel, Thierry, Mikol, Vincent
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 26.07.2002; Elsevier
• Subjects: actinonin; Amidohydrolases; Amino Acid Sequence; Aminopeptidases; Aminopeptidases - chemistry; Anti-Bacterial Agents; Anti-Bacterial Agents - chemistry; antibiotic; Bacillus stearothermophilus; Binding Sites; Catalytic Domain; crystal structure; Crystallography, X-Ray; Escherichia coli; Escherichia coli - enzymology; Geobacillus stearothermophilus - enzymology; Hydroxamic Acids; Hydroxamic Acids - chemistry; inhibitor; Life Sciences; metalloprotease; Models, Molecular; Molecular Sequence Data; Nickel; Nickel - chemistry; Protein Structure, Tertiary; Pseudomonas aeruginosa; Pseudomonas aeruginosa - enzymology; Sequence Analysis, Protein; Sequence Homology, Amino Acid; Staphylococcus aureus; Staphylococcus aureus - enzymology; Vegetal Biology; Zinc; Zinc - chemistry; antibiotic; inhibitor; PDF, peptide deformylase; crystal structure; r.m.s.d., root-mean-square deviation; metalloprotease; actinonin
• ISSN: 0022-2836; 1089-8638
• DOI: 10.1016/S0022-2836(02)00549-1

Bacterial peptide deformylase (PDF) belongs to a sub-family of metalloproteases that catalyse the removal of the N-terminal formyl group from newly synthesised proteins. PDF is essential in prokaryotes and conserved throughout the eubacteria. It is therefore considered an attractive target for developing new antibacterial agents. Here, we report the crystal structures of four bacterial deformylases, free or bound to the naturally occurring antibiotic actinonin, including two from the major bacterial pathogens Pseudomonas aeruginosa and Staphylococcus aureus. The overall tertiary structure is essentially conserved but shows significant differences, namely at the C terminus, which are directly related to the deformylase type (i.e. I or II) they belong to. The geometry around the catalytic metal ion exhibits a high level of similarity within the different enzymes, as does the binding mode of actinonin to the various deformylases. However, some significant structural differences are found in the vicinity of the active site, highlighting the structural and molecular requirements for the design of a deformylase inhibitor active against a broad spectrum of bacterial strains.