1MQY

NMR solution structure of type-B lantibiotics mersacidin in DPC micelles


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 13 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

NMR Study of Mersacidin and Lipid II Interaction in Dodecylphosphocholine Micelles. Conformational Changes are a Key to Antimicrobial Activity

Hsu, S.-T.Breukink, E.Bierbaum, G.Sahl, H.-G.De Kruijff, B.Kaptein, R.Van Nuland, N.A.Bonvin, A.M.

(2003) J Biol Chem 278: 13110

  • DOI: https://doi.org/10.1074/jbc.M211144200
  • Primary Citation of Related Structures:  
    1MQX, 1MQY, 1MQZ

  • PubMed Abstract: 

    Mersacidin belongs to the type B lantibiotics (lanthionine-containing antibiotics) that contain post-translationally modified amino acids and cyclic ring structures. It targets the cell wall precursor lipid II and thereby inhibits cell wall synthesis. In light of the emerging antibiotics resistance problem, the understanding of the antibacterial activity on a structural basis provides a key to circumvent this issue. Here we present solution NMR studies of mersacidin-lipid II interaction in dodecylphosphocholine (DPC) micelles. Distinct solution structures of mersacidin were determined in three different states: in water/methanol solution and in DPC micelles with and without lipid II. The structures in various sample conditions reveal remarkable conformational changes in which the junction between Ala-12 and Abu-13 (where Abu is aminobutyric acid) effectively serves as the hinge for the opening and closure of the ring structures. The DPC micelle-bound form resembles the previously determined NMR and x-ray crystal structures of mersacidin in pure methanol but substantially deviates from the other two states in our current report. The structural changes delineate the large chemical shift perturbations observed during the course of a two-step (15)N-(1)H heteronuclear single quantum coherence titration. They also modulate the surface charge distribution of mersacidin suggesting that electrostatics play a central role in the mersacidin-lipid II interaction. The observed conformational adaptability of mersacidin might be a general feature of lipid II-interacting antibiotics/peptides.


  • Organizational Affiliation

    NMR Department, Bijvoet Center for Biomolecular Research, Utrecht University, 3584CH, Utrecht, The Netherlands.


Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LANTIBIOTIC MERSACIDIN20Bacillus sp. HIL-Y85/54728Mutation(s): 0 
UniProt
Find proteins for P43683 (Bacillus sp. (strain HIL-Y85/54728))
Explore P43683 
Go to UniProtKB:  P43683
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43683
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
DHA
Query on DHA
A
PEPTIDE LINKINGC3 H5 N O2SER
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 1
IDChains NameType/Class2D Diagram3D Interactions
PRD_000199
Query on PRD_000199
A
MersacidinOligopeptide / Antibiotic
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 13 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-03-11
    Type: Initial release
  • Version 1.1: 2009-02-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Other
  • Version 1.4: 2012-12-12
    Changes: Other
  • Version 1.5: 2018-08-08
    Changes: Data collection, Database references, Derived calculations, Experimental preparation