2MH5

Structure and NMR assignments of lantibiotic NAI-107 in DPC micelles


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 80 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Lantibiotic NAI-107 Binds to Bactoprenol-bound Cell Wall Precursors and Impairs Membrane Functions.

Munch, D.Muller, A.Schneider, T.Kohl, B.Wenzel, M.Bandow, J.E.Maffioli, S.Sosio, M.Donadio, S.Wimmer, R.Sahl, H.G.

(2014) J.Biol.Chem. 289: 12063-12076

  • DOI: 10.1074/jbc.M113.537449

  • PubMed Abstract: 
  • The lantibiotic NAI-107 is active against Gram-positive bacteria including vancomycin-resistant enterococci and methicillin-resistant Staphylococcus aureus. To identify the molecular basis of its potency, we studied the mode of action in a series of ...

    The lantibiotic NAI-107 is active against Gram-positive bacteria including vancomycin-resistant enterococci and methicillin-resistant Staphylococcus aureus. To identify the molecular basis of its potency, we studied the mode of action in a series of whole cell and in vitro assays and analyzed structural features by nuclear magnetic resonance (NMR). The lantibiotic efficiently interfered with late stages of cell wall biosynthesis and induced accumulation of the soluble peptidoglycan precursor UDP-N-acetylmuramic acid-pentapeptide (UDP-MurNAc-pentapeptide) in the cytoplasm. Using membrane preparations and a complete cascade of purified, recombinant late stage peptidoglycan biosynthetic enzymes (MraY, MurG, FemX, PBP2) and their respective purified substrates, we showed that NAI-107 forms complexes with bactoprenol-pyrophosphate-coupled precursors of the bacterial cell wall. Titration experiments indicate that first a 1:1 stoichiometric complex occurs, which then transforms into a 2:1 (peptide: lipid II) complex, when excess peptide is added. Furthermore, lipid II and related molecules obviously could not serve as anchor molecules for the formation of defined and stable nisin-like pores, however, slow membrane depolarization was observed after NAI-107 treatment, which could contribute to killing of the bacterial cell.


    Organizational Affiliation

    From the Institute of Medical Microbiology, Immunology and Parasitology, Pharmaceutical Microbiology Section, University of Bonn, 53115 Bonn, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lantibiotic 107891
A
24Microbispora sp. (strain 107891)N/A
Find proteins for P85065 (Microbispora sp. (strain 107891))
Go to UniProtKB:  P85065
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DPV
Query on DPV

Download SDF File 
Download CCD File 
A
dodecyl 2-(trimethylammonio)ethyl phosphate
dodecylphosphocholine
C17 H38 N O4 P
QBHFVMDLPTZDOI-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001219
Query on PRD_001219
ALantibiotic 107891Oligopeptide / Antibiotic

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Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 80 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2014-04-02
    Type: Database references
  • Version 1.2: 2014-05-14
    Type: Database references