9CS1

E. coli BamA beta-barrel bound to darobactin and cyclic peptide CP2

Summary for 9CS1

• Entry DOI: 10.2210/pdb9cs1/pdb
• Related PRD ID: PRD_002330
• Descriptor: Outer membrane protein assembly factor BamA, Cyclic peptide CP2, Darobactin A, ... (5 entities in total)
• Functional Keywords: beta barrel, outer membrane protein, membrane protein
• Biological source: Escherichia coli; More
• Total number of polymer chains: 3
• Total formula weight: 46849.59

Authors

Walker, M.E.,Gu, M.,Lu, J.,Klein, D.J. (deposition date: 2024-07-23, release date: 2025-04-16, Last modification date: 2025-04-23)

Primary citation

Walker, M.E.,Zhu, W.,Peterson, J.H.,Wang, H.,Patteson, J.,Soriano, A.,Zhang, H.,Mayhood, T.,Hou, Y.,Mesbahi-Vasey, S.,Gu, M.,Frost, J.,Lu, J.,Johnston, J.,Hipolito, C.,Lin, S.,Painter, R.E.,Klein, D.,Walji, A.,Weinglass, A.,Kelly, T.M.,Saldanha, A.,Schubert, J.,Bernstein, H.D.,Walker, S.S.
Antibacterial macrocyclic peptides reveal a distinct mode of BamA inhibition.
Nat Commun, 16:3395-3395, 2025

PubMed Abstract: Outer membrane proteins (OMPs) produced by Gram-negative bacteria contain a cylindrical amphipathic β-sheet ("β-barrel") that functions as a membrane spanning domain. The assembly (folding and membrane insertion) of OMPs is mediated by the heterooligomeric β-barrel assembly machine (BAM). The central BAM subunit (BamA) is an attractive antibacterial target because its structure and cell surface localization are conserved, it catalyzes an essential reaction, and potent bactericidal compounds that inhibit its activity have been described. Here we utilize mRNA display to discover cyclic peptides that bind to Escherichia coli BamA with high affinity. We describe three peptides that arrest the growth of BAM deficient E. coli strains, inhibit OMP assembly in live cells and in vitro, and bind to unique sites within the BamA β-barrel lumen. Remarkably, we find that if the peptides are added to cultures after a slowly assembling OMP mutant binds to BamA, they accelerate its biogenesis. The data strongly suggest that the peptides trap BamA in conformations that block the initiation of OMP assembly but favor a later assembly step. Molecular dynamics simulations provide further evidence that the peptides bind stably to BamA and function by a previously undescribed mechanism.

PubMed: 40210867
DOI: 10.1038/s41467-025-58086-w

Experimental method

X-RAY DIFFRACTION (2.147 Å)