Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

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

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

Macromolecule Content

• Total Structure Weight: 0.79 kDa 
• Atom Count: 55 
• Modelled Residue Count: 8 
• Deposited Residue Count: 8 
• Unique protein chains: 1

6QYV

Solution NMR of synthetic analogues of nisin and mutacin ring A and ring B - Mutacin I Ring A (Ser2, Ala5, Ala8) analogue

• PDB DOI: 10.2210/pdb6QYV/pdb
• BMRB: 34373

• Classification: ANTIBIOTIC
• Organism(s): Lactococcus lactis
• Mutation(s): No 


• Deposited: 2019-03-09 Released: 2019-09-11 
• Deposition Author(s): Dickman, R., Mitchell, S.A., Figueiredo, A., Hansen, D.F., Tabor, A.B.
• Funding Organization(s): Engineering and Physical Sciences Research Council

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy 

Literature

Molecular Recognition of Lipid II by Lantibiotics: Synthesis and Conformational Studies of Analogues of Nisin and Mutacin Rings A and B.

Dickman, R., Mitchell, S.A., Figueiredo, A.M., Hansen, D.F., Tabor, A.B.

(2019) J Org Chem 84: 11493-11512

• PubMed: 31464129 
• DOI: 10.1021/acs.joc.9b01253
• Primary Citation of Related Structures:  
  6QM1, 6QTF, 6QYR, 6QYS, 6QYT, 6QYU, 6QYV, 6QYW


• PubMed Abstract: 
  

In response to the growing threat posed by antibiotic-resistant bacterial strains, extensive research is currently focused on developing antimicrobial agents that target lipid II, a vital precursor in the biosynthesis of bacterial cell walls. The lantibiotic nisin and related peptides display unique and highly selective binding to lipid II. A key feature of the nisin-lipid II interaction is the formation of a cage-like complex between the pyrophosphate moiety of lipid II and the two thioether-bridged rings, rings A and B, at the N-terminus of nisin. To understand the important structural factors underlying this highly selective molecular recognition, we have used solid-phase peptide synthesis to prepare individual ring A and B structures from nisin, the related lantibiotic mutacin, and synthetic analogues. Through NMR studies of these rings, we have demonstrated that ring A is preorganized to adopt the correct conformation for binding lipid II in solution and that individual amino acid substitutions in ring A have little effect on the conformation. We have also analyzed the turn structures adopted by these thioether-bridged peptides and show that they do not adopt the tight α-turn or β-turn structures typically found in proteins.

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Related Citations: 

• A chemical biology approach to understanding molecular recognition of lipid II by nisin: Solid-phase synthesis and NMR ensemble analysis of nisin(1-12) and a synthetic ana-logue.
  Dickman, R., Danelius, E., Mitchell, S.A., Hansen, D.F., Erdelyi, M., Tabor, A.B.
  () To be published --: --

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Organizational Affiliation: 

Department of Chemistry , University College London , 20 Gordon Street , London WC1H 0AJ , U.K.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHE-SER-DAL-LEU-ALA-LEU-CYS-ALA	A	8	Lactococcus lactis	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 15 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 6QYV Olderado

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-03-09 
• Released Date: 2019-09-11 
Deposition Author(s): Dickman, R., Mitchell, S.A., Figueiredo, A., Hansen, D.F., Tabor, A.B.

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Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	EP/L504889/1

Revision History  

• Version 1.0: 2019-09-11
  Type: Initial release
  
• Version 1.1: 2019-10-02
  Changes: Data collection, Database references