7T3H | pdb_00007t3h

MicroED structure of Dynobactin

• PDB DOI: https://doi.org/10.2210/pdb7T3H/pdb

• Classification: ANTIBIOTIC
• Organism(s): Photorhabdus australis
• Mutation(s): No 


• Deposited: 2021-12-07 Released: 2022-10-19 
• Deposition Author(s): Yoo, B.-K., Kaiser, J.T., Rees, D.C., Miller, R.D., Iinishi, A., Lewis, K., Bowman, S.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 1.05 Å
• R-Value Work: 
  0.190 (DCC) 
• R-Value Observed: 
  0.129 (Depositor) 

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

• PubMed: 36163500 
• DOI: https://doi.org/10.1038/s41564-022-01227-4
• Primary Citation 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.

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Organizational Affiliation: 
• Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA.
Biozentrum, University of Basel, Basel, Switzerland.
Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
Beckman Institute, California Institute of Technology, Pasadena, CA, USA.
National Crystallization Center, Hauptman-Woodward Medical Research Institute, Buffalo, NY, USA.
Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA.
Biozentrum, University of Basel, Basel, Switzerland. [e-mail].
Antimicrobial Discovery Center, Department of Biology, Northeastern University, Boston, MA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: mass spectrometry

Macromolecule Content 

• Total Structure Weight: 1.31 kDa 
• Atom Count: 102 
• Modeled Residue Count: 10 
• Deposited Residue Count: 10 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TRP-ASN-SER-ASN-VAL-HIS-SER-TYR-ARG-PHE	A	10	Photorhabdus australis	Mutation(s): 0
UniProt
Find proteins for A0A1C0U7H2 (Photorhabdus australis subsp. thailandensis) Explore A0A1C0U7H2  Go to UniProtKB:  A0A1C0U7H2

Experimental Data & Validation

Experimental Data

• Method: ELECTRON CRYSTALLOGRAPHY
• Resolution: 1.05 Å
• R-Value Work:  0.190 (DCC) 
• R-Value Observed: 0.129 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.23	α = 90
b = 9.73	β = 112
c = 19.07	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
SHELX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-10-19 
Deposition Author(s): Yoo, B.-K., Kaiser, J.T., Rees, D.C., Miller, R.D., Iinishi, A., Lewis, K., Bowman, S.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation		177084
Swiss National Science Foundation		187170

Revision History  

• Version 1.0: 2022-10-19
  Type: Initial release
  
• Version 1.1: 2024-11-20
  Changes: Data collection, Structure summary