7UGW image
Entry Detail
PDB ID:
7UGW
Title:
M. tuberculosis DNA gyrase cleavage core bound to DNA and evybactin
Biological Source:
PDB Version:
Deposition Date:
2022-03-25
Release Date:
2022-08-17
Method Details:
Experimental Method:
Resolution:
3.00 Å
R-Value Free:
0.27
R-Value Work:
0.21
R-Value Observed:
0.22
Space Group:
P 21 21 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:DNA gyrase subunit A
Mutations:Y129F
Chain IDs:A, C
Chain Length:500
Number of Molecules:2
Biological Source:Mycobacterium tuberculosis H37Rv
Polymer Type:polypeptide(L)
Description:DNA gyrase subunit B
Chain IDs:B, D
Chain Length:251
Number of Molecules:2
Biological Source:Mycobacterium tuberculosis H37Rv
Polymer Type:polypeptide(L)
Description:evybactin
Chain IDs:F (auth: E)
Chain Length:12
Number of Molecules:1
Biological Source:Photorhabdus noenieputensis
Polymer Type:polydeoxyribonucleotide
Description:DNA (46-MER)
Chain IDs:E (auth: V)
Chain Length:46
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
Peptide-like Molecules
PRD_002540
Primary Citation
Evybactin is a DNA gyrase inhibitor that selectively kills Mycobacterium tuberculosis.
Nat.Chem.Biol. 18 1236 1244 (2022)
PMID: 35996001 DOI: 10.1038/s41589-022-01102-7

Abstact

The antimicrobial resistance crisis requires the introduction of novel antibiotics. The use of conventional broad-spectrum compounds selects for resistance in off-target pathogens and harms the microbiome. This is especially true for Mycobacterium tuberculosis, where treatment requires a 6-month course of antibiotics. Here we show that a novel antimicrobial from Photorhabdus noenieputensis, which we named evybactin, is a potent and selective antibiotic acting against M. tuberculosis. Evybactin targets DNA gyrase and binds to a site overlapping with synthetic thiophene poisons. Given the conserved nature of DNA gyrase, the observed selectivity against M. tuberculosis is puzzling. We found that evybactin is smuggled into the cell by a promiscuous transporter of hydrophilic compounds, BacA. Evybactin is the first, but likely not the only, antimicrobial compound found to employ this unusual mechanism of selectivity.

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Primary Citation of related structures