Crystallographic Analysis of Bacterial Signal Peptidase in Ternary Complex with Arylomycin A2 and a β-Sultam Inhibitor

• Published in: Biochemistry (Easton) Vol. 48; no. 38; pp. 8976 - 8984
• Main Authors: Luo, Chuanyun, Roussel, Patrick, Dreier, Jürg, Page, Malcolm G.P, Paetzel, Mark
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 29-09-2009
• Subjects: Catalytic Domain; Crystallography, X-Ray; Escherichia coli Proteins - antagonists & inhibitors; Escherichia coli Proteins - chemistry; Kinetics; Macromolecular Substances; Membrane Proteins - antagonists & inhibitors; Membrane Proteins - chemistry; Models, Molecular; Molecular Structure; Oligopeptides - chemistry; Oligopeptides - pharmacology; Peptide Fragments - antagonists & inhibitors; Peptide Fragments - chemistry; Serine Endopeptidases - chemistry; Serine Proteinase Inhibitors - chemistry; Serine Proteinase Inhibitors - pharmacology; Static Electricity; Sulfonamides - chemistry; Sulfonamides - pharmacology
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi9009538

Bacterial type I signal peptidase (SPase I), an essential membrane-bound endopeptidase with a unique Ser/Lys dyad mechanism, is being investigated as a potential novel antibiotic target. We present here binding and inhibition assays along with crystallographic data that shows that the lipohexapeptide-based natural product arylomycin A2 and the morpholino-β-sultam derivative (BAL0019193) inhibit SPase I by binding to non-overlapping subsites near the catalytic center. The 2.0 Å resolution crystal structure of the soluble catalytic domain of Escherichia coli SPase I (SPase I Δ2−75) in ternary complex with arylomycin A2 and BAL0019193 reveals the position of BAL0019193 adjacent to arylomycin A2 within the SPase I binding site. BAL0019193 binds in a noncovalent manner in close proximity to SPase I residues Ser88, Ser90, Lys145, Asn277, Ala279, and Glu307, as well as atom O45 of arylomycin A2. The binding mode of arylomycin A2 in this 2.0 Å resolution ternary complex is compared to that seen in the previous 2.5 Å resolution arylomycin A2-SPase cocrystal structure. This work contributes to our understanding of SPase I inhibitor/substrate recognition and should prove helpful in the further development of novel antibiotics based on the inhibition of SPase I.