7Z9C | pdb_00007z9c

E.coli gyrase holocomplex with 217 bp DNA and albicidin

• PDB DOI: https://doi.org/10.2210/pdb7Z9C/pdb
• NAKB: 7Z9C
• EM Map EMD-14570: EMDB EMDataResource

• Classification: ISOMERASE
• Organism(s): Escherichia coli str. K-12 substr. MG1655, Escherichia phage Mu
• Expression System: Escherichia coli BL21(DE3), Escherichia coli
• Mutation(s): No 


• Deposited: 2022-03-21 Released: 2023-02-15 
• Deposition Author(s): Ghilarov, D., Heddle, J.G.H., Suessmuth, R.
• Funding Organization(s): Wellcome Trust, Polish National Science Centre

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.06 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 7Z9G 7Z9K 7Z9M

Literature

Molecular mechanism of topoisomerase poisoning by the peptide antibiotic albicidin.

Michalczyk, E., Hommernick, K., Behroz, I., Kulike, M., Pakosz-Stepien, Z., Mazurek, L., Seidel, M., Kunert, M., Santos, K., von Moeller, H., Loll, B., Weston, J.B., Mainz, A., Heddle, J.G., Sussmuth, R.D., Ghilarov, D.

(2023) Nat Catal 6: 52-67

• PubMed: 36741192 
• DOI: https://doi.org/10.1038/s41929-022-00904-1
• Primary Citation Related Structures: 
  7Z9C, 7Z9G, 7Z9K, 7Z9M


• PubMed Abstract: 
  

  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 Escherichia coli 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 E. coli 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.

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Organizational Affiliation: 
• Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
Institut für Chemie, Technische Universität Berlin, Berlin, Germany.
Postgraduate School of Molecular Medicine, Warsaw, Poland.
moloX GmbH, Berlin, Germany.
Institut für Chemie und Biochemie, Freie Universität Berlin, Berlin, Germany.
John Innes Centre, Norwich Research Park, Norwich, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 397.97 kDa 
• Atom Count: 15,966 
• Modeled Residue Count: 1,902 
• Deposited Residue Count: 3,448 
• Unique protein chains: 2
• Unique nucleic acid chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit A	A, C	881	Escherichia coli str. K-12 substr. MG1655	Mutation(s): 0  Gene Names: gyrA, hisW, nalA, parD, b2231, JW2225 EC: 5.6.2.2
UniProt
Find proteins for P0AES4 (Escherichia coli (strain K12)) Explore P0AES4  Go to UniProtKB:  P0AES4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B	B, D	811	Escherichia coli str. K-12 substr. MG1655	Mutation(s): 0  Gene Names: gyrB, acrB, cou, himB, hisU, nalC, parA, pcbA, b3699, JW5625 EC: 5.6.2.2
UniProt
Find proteins for P0AES6 (Escherichia coli (strain K12)) Explore P0AES6  Go to UniProtKB:  P0AES6

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*AP*AP*TP*CP*TP*GP*TP*GP*CP*GP*GP*GP*T)-3')	E	14	Escherichia phage Mu

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*GP*AP*AP*TP*CP*AP*GP*GP*CP*AP*TP*AP*A)-3')	F	14	Escherichia phage Mu

Entity ID: 5
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*TP*CP*AP*CP*CP*CP*GP*CP*AP*CP*AP*GP*AP*TP*TP*T)-3')	G	18	Escherichia phage Mu

Entity ID: 6
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*AP*TP*TP*TP*TP*AP*TP*GP*CP*CP*TP*GP*AP*TP*TP*CP*T)-3')	H	18	Escherichia phage Mu

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BWH (Subject of Investigation/LOI)	J [auth C]	albicidin C44 H38 N6 O12 NZSWNNDHPOTJNH-VEJILBAHSA-N
MG	I [auth B], K [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	A, C	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.06 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-02-15 
Deposition Author(s): Ghilarov, D., Heddle, J.G.H., Suessmuth, R.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	221868/Z/20/Z
Polish National Science Centre	Poland	2020/39/B/NZ1/02898

Revision History  

• Version 1.0: 2023-02-15
  Type: Initial release
  
• Version 1.1: 2023-07-19
  Changes: Author supporting evidence
• Version 1.2: 2024-11-13
  Changes: Data collection, Structure summary
• Version 1.3: 2025-07-09
  Changes: Data collection