7T3H

MicroED structure of Dynobactin


Experimental Data Snapshot

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 1.05 Å
  • R-Value Observed: 0.129 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Computational identification of a systemic antibiotic for gram-negative bacteria.

Miller, R.D.Iinishi, A.Modaresi, S.M.Yoo, B.K.Curtis, T.D.Lariviere, P.J.Liang, L.Son, S.Nicolau, S.Bargabos, R.Morrissette, M.Gates, M.F.Pitt, N.Jakob, R.P.Rath, P.Maier, T.Malyutin, A.G.Kaiser, J.T.Niles, S.Karavas, B.Ghiglieri, M.Bowman, S.E.J.Rees, D.C.Hiller, S.Lewis, K.

(2022) Nat Microbiol 7: 1661-1672

  • DOI: https://doi.org/10.1038/s41564-022-01227-4
  • Primary Citation of Related Structures:  
    7R1V, 7R1W, 7T3H

  • PubMed Abstract: 

    Discovery of antibiotics acting against Gram-negative species is uniquely challenging due to their restrictive penetration barrier. BamA, which inserts proteins into the outer membrane, is an attractive target due to its surface location. Darobactins produced by Photorhabdus, a nematode gut microbiome symbiont, target BamA. We reasoned that a computational search for genes only distantly related to the darobactin operon may lead to novel compounds. Following this clue, we identified dynobactin A, a novel peptide antibiotic from Photorhabdus australis containing two unlinked rings. Dynobactin is structurally unrelated to darobactins, but also targets BamA. Based on a BamA-dynobactin co-crystal structure and a BAM-complex-dynobactin cryo-EM structure, we show that dynobactin binds to the BamA lateral gate, uniquely protruding into its β-barrel lumen. Dynobactin showed efficacy in a mouse systemic Escherichia coli infection. This study demonstrates the utility of computational approaches to antibiotic discovery and suggests that dynobactin is a promising lead for drug development.


  • Organizational Affiliation

    Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRP-ASN-SER-ASN-VAL-HIS-SER-TYR-ARG-PHE10Photorhabdus australisMutation(s): 0 
UniProt
Find proteins for A0A1C0U7H2 (Photorhabdus australis subsp. thailandensis)
Explore A0A1C0U7H2 
Go to UniProtKB:  A0A1C0U7H2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1C0U7H2
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON CRYSTALLOGRAPHY
  • Resolution: 1.05 Å
  • R-Value Observed: 0.129 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.23α = 90
b = 9.73β = 112
c = 19.07γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
SHELXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science Foundation177084
Swiss National Science Foundation187170

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-19
    Type: Initial release