7P1C

Crystal structure of E.coli BamA beta-barrel in complex with darobactin B


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Mutasynthetic Production and Antimicrobial Characterization of Darobactin Analogs.

Bohringer, N.Green, R.Liu, Y.Mettal, U.Marner, M.Modaresi, S.M.Jakob, R.P.Wuisan, Z.G.Maier, T.Iinishi, A.Hiller, S.Lewis, K.Schaberle, T.F.

(2021) Microbiol Spectr 9: e0153521-e0153521

  • DOI: https://doi.org/10.1128/spectrum.01535-21
  • Primary Citation of Related Structures:  
    7P1C

  • PubMed Abstract: 

    There is great need for therapeutics against multidrug-resistant, Gram-negative bacterial pathogens. Recently, darobactin A, a novel bicyclic heptapeptide that selectively kills Gram-negative bacteria by targeting the outer membrane protein BamA, was discovered. Its efficacy was proven in animal infection models of Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa, thus promoting darobactin A as a promising lead compound. Originally discovered from members of the nematode-symbiotic genus Photorhabdus , the biosynthetic gene cluster (BGC) encoding the synthesis of darobactin A can also be found in other members of the class Gammaproteobacteria . Therein, the precursor peptides DarB to -F, which differ in their core sequence from darobactin A, were identified in silico . Even though production of these analogs was not observed in the putative producer strains, we were able to generate them by mutasynthetic derivatization of a heterologous expression system. The analogs generated were isolated and tested for their bioactivity. The most potent compound, darobactin B, was used for cocrystallization with the target BamA, revealing a binding site identical to that of darobactin A. Despite its potency, darobactin B did not exhibit cytotoxicity, and it was slightly more active against Acinetobacter baumannii isolates than darobactin A. Furthermore, we evaluated the plasma protein binding of darobactin A and B, indicating their different pharmacokinetic properties. This is the first report on new members of this new antibiotic class, which is likely to expand to several promising therapeutic candidates. IMPORTANCE Therapeutic options to combat Gram-negative bacterial pathogens are dwindling with increasing antibiotic resistance. This study presents a proof of concept for the heterologous-expression approach to expand on the novel antibiotic class of darobactins and to generate analogs with different activities and pharmacokinetic properties. In combination with the structural data of the target BamA, this approach may contribute to structure-activity relationship (SAR) data to optimize inhibitors of this essential outer membrane protein of Gram-negative pathogens.


  • Organizational Affiliation

    Justus-Liebig-University Gießen, Gießen, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Outer membrane protein assembly factor BamA392Escherichia coli O157:H7Mutation(s): 2 
Gene Names: bamAyaeTZ0188ECs0179
Membrane Entity: Yes 
UniProt
Find proteins for P0A940 (Escherichia coli (strain K12))
Explore P0A940 
Go to UniProtKB:  P0A940
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A940
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TRP-ASN-UX8-THR-LYS-ARG-PHE7synthetic constructMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.234 
  • Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.56α = 90
b = 80.372β = 107.94
c = 89.247γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Derived calculations, Refinement description