4K7T | pdb_00004k7t

Structure of the ternary complex of bacitracin, zinc, and geranyl-pyrophosphate

• PDB DOI: https://doi.org/10.2210/pdb4K7T/pdb

• Classification: ANTIBIOTIC
• Organism(s): Bacillus subtilis
• Mutation(s): No 


• Deposited: 2013-04-17 Released: 2013-08-14 
• Deposition Author(s): Economou, N.J., Loll, P.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.149 (Depositor), 0.155 (DCC) 
• R-Value Work: 
  0.127 (Depositor), 0.136 (DCC) 
• R-Value Observed: 
  0.128 (Depositor) 

Literature

High-resolution crystal structure reveals molecular details of target recognition by bacitracin.

Economou, N.J., Cocklin, S., Loll, P.J.

(2013) Proc Natl Acad Sci U S A 110: 14207-14212

• PubMed: 23940351 
• DOI: https://doi.org/10.1073/pnas.1308268110
• Primary Citation Related Structures: 
  4K7T


• PubMed Abstract: 
  

  Bacitracin is a metalloantibiotic agent that is widely used as a medicine and feed additive. It interferes with bacterial cell-wall biosynthesis by binding undecaprenyl-pyrophosphate, a lipid carrier that serves as a critical intermediate in cell wall production. Despite bacitracin's broad use, the molecular details of its target recognition have not been elucidated. Here we report a crystal structure for the ternary complex of bacitracin A, zinc, and a geranyl-pyrophosphate ligand at a resolution of 1.1 Å. The antibiotic forms a compact structure that completely envelopes the ligand's pyrophosphate group, together with flanking zinc and sodium ions. The complex adopts a highly amphipathic conformation that offers clues to antibiotic function in the context of bacterial membranes. Bacitracin's efficient sequestration of its target represents a previously unseen mode for the recognition of lipid pyrophosphates, and suggests new directions for the design of next-generation antimicrobial agents.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 1.86 kDa 
• Atom Count: 141 
• Modeled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
bacitracin A2	A	12	Bacillus subtilis	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GPP	B [auth A]	GERANYL DIPHOSPHATE C10 H20 O7 P2 GVVPGTZRZFNKDS-JXMROGBWSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001070	A	Bacitracin A1	Cyclic peptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.149 (Depositor), 0.155 (DCC) 
• R-Value Work:  0.127 (Depositor), 0.136 (DCC) 
• R-Value Observed: 0.128 (Depositor) 

Space Group: P 6₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.98	α = 90
b = 35.98	β = 90
c = 16.12	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-08-14 
Deposition Author(s): Economou, N.J., Loll, P.J.

Revision History  

• Version 1.0: 2013-08-14
  Type: Initial release
  
• Version 1.1: 2013-09-18
  Changes: Database references
• Version 1.2: 2013-10-16
  Changes: Derived calculations
• Version 1.3: 2024-10-16
  Changes: Data collection, Database references, Derived calculations, Structure summary