High-resolution crystal structure reveals molecular details of target recognition by bacitracin

Abstract

Bacitracin is a metalloantibiotic agent that is widely used as a medicine and feed additive. It interferes with bacterial cell-wall biosynthesis by binding undecaprenyl-pyrophosphate, a lipid carrier that serves as a critical intermediate in cell wall production. Despite bacitracin’s broad use, the molecular details of its target recognition have not been elucidated. Here we report a crystal structure for the ternary complex of bacitracin A, zinc, and a geranyl-pyrophosphate ligand at a resolution of 1.1 Å. The antibiotic forms a compact structure that completely envelopes the ligand’s pyrophosphate group, together with flanking zinc and sodium ions. The complex adopts a highly amphipathic conformation that offers clues to antibiotic function in the context of bacterial membranes. Bacitracin’s efficient sequestration of its target represents a previously unseen mode for the recognition of lipid pyrophosphates, and suggests new directions for the design of next-generation antimicrobial agents.

Proposed Carrier Lipid-binding Site of Undecaprenyl Pyrophosphate Phosphatase from Escherichia coli

“…The polypeptide antibiotic bacitracin has been shown to inhibit the bacterial cell wall synthesis through the sequestration of the pyrophosphate moiety of C 55 -PP (37,38). Therefore, the inhibition of E. coli UppP by bacitracin has also been determined (Fig.…”

Depletion of Undecaprenyl Pyrophosphate Phosphatases Disrupts Cell Envelope Biogenesis in Bacillus subtilis

“…Compounds that inhibit the recycling of UPP may also serve as effective antibiotics. The most widely used antibiotic of this class is bacitracin, which binds tightly to the pyrophosphate group on surface-exposed UPP to inhibit its dephosphorylation (18). Bacitracin also activates the M stress response, which contributes to bacitracin resistance by increasing the synthesis of BcrC (19)(20)(21), a predicted UPP-Pase presumed to act on the outer face of the membrane to convert UPP (the target of bacitracin) into Und-P (22).…”

Characterization of Two Component Systems of Lactobacillus casei BL23 and their involvement in stress response

“…After removal of the peptidoglycan precursors, the lipid carrier remains in the pyrophosphate form (UPP), which is dephosphorylated by UPPphosphatases (Bouhss et al, 2008) and flipped back to the cytoplasmic face of the membrane (Figure 4). This recycling step is inhibited by bacitracin, which tightly binds to the pyrophosphate group and thus prevents the dephosphorylation reaction (Figure 4) (Siewert and Strominger, 1967;Storm and Strominger, 1973;Schneider and Sahl, 2010;Economou et al, 2013). …”

“…This leads to the dissipation of membrane potential and the efflux of small metabolites from the target cell. Many bacteria also produce non-ribosomally synthesized peptides such as the small circular metallo-peptide bacitracin ( Figure 7) (Johnson et al, 1945;Economou et al, 2013), or lipodepsipeptides such as ramoplanin ( Figure 7) or enduracidin (Fang et al, 2006).…”

“…pore-formation by nisin-type lantibiotics (Figure 8) (Schneider and Sahl, 2010;Scherer et al, 2013) or disturbance of membrane function by bacitracin ( Figure 4 and Figure 9)) (Ming and Epperson, 2002;Schneider and Sahl, 2010;Economou et al, 2013).…”