2N5Y

Solution NMR structure of octyl-tridecaptin A1 in DPC micelles containing Gram-negative lipid II

• PDB DOI: https://doi.org/10.2210/pdb2N5Y/pdb
• BMRB: 25741

• Classification: ANTIMICROBIAL PROTEIN
• Mutation(s): No 


• Deposited: 2015-08-03 Released: 2016-09-28 
• Deposition Author(s): Cochrane, S.A., Findlay, B., Bakhtiary, A., Rodriguez-Lopez, E.M., Vederas, J.C.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

Antimicrobial lipopeptide tridecaptin A1 selectively binds to Gram-negative lipid II.

Cochrane, S.A., Findlay, B., Bakhtiary, A., Acedo, J.Z., Rodriguez-Lopez, E.M., Mercier, P., Vederas, J.C.

(2016) Proc Natl Acad Sci U S A 113: 11561-11566

• PubMed: 27688760 
• DOI: https://doi.org/10.1073/pnas.1608623113
• Primary Citation of Related Structures:  
  2N5W, 2N5Y


• PubMed Abstract: 
  

  Tridecaptin A ₁ (TriA ₁ ) is a nonribosomal lipopeptide with selective antimicrobial activity against Gram-negative bacteria. Here we show that TriA ₁ exerts its bactericidal effect by binding to the bacterial cell-wall precursor lipid II on the inner membrane, disrupting the proton motive force. Biochemical and biophysical assays show that binding to the Gram-negative variant of lipid II is required for membrane disruption and that only the proton gradient is dispersed. The NMR solution structure of TriA ₁ in dodecylphosphocholine micelles with lipid II has been determined, and molecular modeling was used to provide a structural model of the TriA ₁ -lipid II complex. These results suggest that TriA ₁ kills Gram-negative bacteria by a mechanism of action using a lipid-II-binding motif.

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Organizational Affiliation: 

Department of Chemistry, University of Alberta, Edmonton, AB, Canada T6G 2G2.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 1.52 kDa 
• Atom Count: 107 
• Modelled Residue Count: 13 
• Deposited Residue Count: 13 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Octyl-tridecaptin A1	A	13	N/A	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DAB	A	L-PEPTIDE LINKING	C4 H10 N2 O2		ALA

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-28 
Deposition Author(s): Cochrane, S.A., Findlay, B., Bakhtiary, A., Rodriguez-Lopez, E.M., Vederas, J.C.

Revision History  

• Version 1.0: 2016-09-28
  Type: Initial release
  
• Version 1.1: 2016-10-19
  Changes: Database references
• Version 1.2: 2016-10-26
  Changes: Database references
• Version 2.0: 2023-11-15
  Changes: Atomic model, Data collection, Database references, Derived calculations