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Structure paper

TitleMolecular mechanism of topoisomerase poisoning by the peptide antibiotic albicidin.
Journal, issue, pagesNat Catal, Vol. 6, Issue 1, Page 52-67, Year 2023
Publish dateJan 23, 2023
AuthorsElizabeth Michalczyk / Kay Hommernick / Iraj Behroz / Marcel Kulike / Zuzanna Pakosz-Stępień / Lukasz Mazurek / Maria Seidel / Maria Kunert / Karine Santos / Holger von Moeller / Bernhard Loll / John B Weston / Andi Mainz / Jonathan G Heddle / Roderich D Süssmuth / Dmitry Ghilarov /
PubMed AbstractThe peptide antibiotic albicidin is a DNA topoisomerase inhibitor with low-nanomolar bactericidal activity towards fluoroquinolone-resistant Gram-negative pathogens. However, its mode of action is ...The peptide antibiotic albicidin is a DNA topoisomerase inhibitor with low-nanomolar bactericidal activity towards fluoroquinolone-resistant Gram-negative pathogens. However, its mode of action is poorly understood. We determined a 2.6 Å resolution cryoelectron microscopy structure of a ternary complex between topoisomerase DNA gyrase, a 217 bp double-stranded DNA fragment and albicidin. Albicidin employs a dual binding mechanism where one end of the molecule obstructs the crucial gyrase dimer interface, while the other intercalates between the fragments of cleaved DNA substrate. Thus, albicidin efficiently locks DNA gyrase, preventing it from religating DNA and completing its catalytic cycle. Two additional structures of this trapped state were determined using synthetic albicidin analogues that demonstrate improved solubility, and activity against a range of gyrase variants and topoisomerase IV. The extraordinary promiscuity of the DNA-intercalating region of albicidins and their excellent performance against fluoroquinolone-resistant bacteria holds great promise for the development of last-resort antibiotics.
External linksNat Catal / PubMed:36741192 / PubMed Central
MethodsEM (single particle)
Resolution3.06 - 3.3 Å
Structure data

14570

7z9c

EMDB-14570, PDB-7z9c:
E.coli gyrase holocomplex with 217 bp DNA and albicidin
Method: EM (single particle) / Resolution: 3.06 Å

14572

7z9g

EMDB-14572, PDB-7z9g:
E.coli gyrase holocomplex with 217 bp DNA and Albi-2
Method: EM (single particle) / Resolution: 3.25 Å

14573

7z9k

EMDB-14573, PDB-7z9k:
E.coli gyrase holocomplex with 217 bp DNA and Albi-1 (site TG)
Method: EM (single particle) / Resolution: 3.25 Å

14574

7z9m

EMDB-14574, PDB-7z9m:
E.coli gyrase holocomplex with 217 bp DNA and Albi-1 (site AA)
Method: EM (single particle) / Resolution: 3.3 Å

Chemicals

ChemComp-MG:
Unknown entry

ChemComp-BWH:
albicidin

ChemComp-HOH:
WATER / Water

ChemComp-IM0:
4-[[3-(2-azanylethoxy)-2-oxidanyl-4-[[5-[[(2~{S})-2-[[4-[(6-oxidanylnaphthalen-2-yl)carbonylamino]phenyl]carbonylamino]-3-(1~{H}-1,2,3-triazol-4-yl)propanoyl]amino]pyridin-2-yl]carbonylamino]phenyl]carbonylamino]-3-methoxy-2-oxidanyl-benzoic acid

ChemComp-IL1:
4-[[4-[[5-[[(2S)-2-[[5-[(4-cyanophenyl)carbonylamino]pyridin-2-yl]carbonylamino]-3-(1H-1,2,3-triazol-4-yl)propanoyl]amino]pyridin-2-yl]carbonylamino]-2-oxidanyl-3-propan-2-yloxy-phenyl]carbonylamino]benzoic acid

Source
  • escherichia coli str. k-12 substr. mg1655 (bacteria)
  • escherichia phage mu (virus)
KeywordsISOMERASE / type II topoisomerase / antibiotic / albicidin / DNA gyrase

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