2N5W | pdb_00002n5w

The NMR solution structure of octyl-tridecaptin A1 in DPC micelles

• PDB DOI: https://doi.org/10.2210/pdb2N5W/pdb
• BMRB: 25737

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


• Deposited: 2015-08-01 Released: 2016-09-28 
• Deposition Author(s): Cochrane, S.A., Findlay, B., Bakhtiary, A., Acedo, J.Z., 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 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.
National High Field NMR Centre, University of Alberta, Edmonton, AB, Canada T6G 2E1.
Department of Chemistry, University of Alberta, Edmonton, AB, Canada T6G 2G2; [e-mail].

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 
• Modeled 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
28J	A	D-PEPTIDE LINKING	C6 H13 N O2		--
4FO	A	D-PEPTIDE LINKING	C4 H10 N2 O2		--
4N3	A	D-PEPTIDE LINKING	C13 H25 N O3		--
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., Acedo, J.Z., 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