6B34 | pdb_00006b34

NMR ensemble of Tyrocidine A analogue AC3.27

• PDB DOI: https://doi.org/10.2210/pdb6B34/pdb
• BMRB: 30346

• Classification: ANTIMICROBIAL PROTEIN
• Organism(s): Brevibacillus brevis
• Mutation(s): No 


• Deposited: 2017-09-20 Released: 2017-12-06 
• Deposition Author(s): Cameron, A.J., Ewdards, P.J.B., Harjes, E., Sarojini, V.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 10 
• Conformers Submitted: 9 
• Selection Criteria: structures with acceptable covalent geometry 

Literature

Tyrocidine A Analogues Bearing the Planar d-Phe-2-Abz Turn Motif: How Conformation Impacts Bioactivity.

Cameron, A.J., Edwards, P.J.B., Harjes, E., Sarojini, V.

(2017) J Med Chem 60: 9565-9574

• PubMed: 29140694 
• DOI: https://doi.org/10.1021/acs.jmedchem.7b00953
• Primary Citation Related Structures: 
  6B34, 6B35


• PubMed Abstract: 
  

  The d-Phe-Pro β-turn of the cyclic β-hairpin antimicrobial decapeptide tyrocidine A, (Tyrc A) was substituted with the d-Phe-2-aminobenzoic acid (2-Abz) motif in a synthetic analogue (1). The NMR structure of 1 demonstrated that compound 1 retained the β-hairpin structure of Tyrc A with additional planarity, resulting in approximately 30-fold reduced hemolysis than Tyrc A. Although antibacterial activity was partially compromised, a single Gln to Lys substitution (2) restored activity equivalent to Tyrc A against S. aureus, enhanced activity against two Gram negative strains and maintained the reduced hemeloysis of 1. Analysis by transmission electron microscopy (TEM) suggested a membrane lytic mechanism of action for these peptides. Compound 2 also exhibits nanomolar antifungal activity in synergy with amphotericin B. The d-Phe-2-Abz turn may serve as a tool for the synthesis of structurally predictable β-hairpin libraries. Unlike traditional β-turn motifs such as d-Pro-Gly, both the 2-Abz and d-Phe rings may be further functionalized.

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Organizational Affiliation: 
• School of Chemical Sciences, University of Auckland , Auckland 1142, New Zealand.
Institute of Fundamental Sciences, Massey University , Palmerston North 4442, New Zealand.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 1.31 kDa 
• Atom Count: 94 
• Modeled Residue Count: 10 
• Deposited Residue Count: 10 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrocidine A analogue D-PHE-BE2-PHE-D-PHE-ASN-GLN-TYR-VAL-ORN-LEU	A	10	Brevibacillus brevis	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
BE2	A	L-PEPTIDE LINKING	C7 H7 N O2		--
DPN	A	D-PEPTIDE LINKING	C9 H11 N O2		--
ORN	A	L-PEPTIDE LINKING	C5 H12 N2 O2		ALA

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 1
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002289	A	Tyrocidine A analogue (DPN)(BE2)F(DPN)NQYV(ORN)L	Cyclic peptide / Antibiotic

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 10 
• Conformers Submitted: 9 
• Selection Criteria: structures with acceptable covalent geometry 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-06 
Deposition Author(s): Cameron, A.J., Ewdards, P.J.B., Harjes, E., Sarojini, V.

Revision History  

• Version 1.0: 2017-12-06
  Type: Initial release
  
• Version 1.1: 2017-12-27
  Changes: Database references
• Version 2.0: 2020-08-12
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-06-14
  Changes: Database references, Other
• Version 3.0: 2023-11-15
  Changes: Atomic model, Data collection, Derived calculations