1WCO

The solution structure of the nisin-lipid II complex


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: RMSD CLUSTERING AND LOWEST TOTAL ENERGY 

wwPDB Validation 3D Report Full Report



Literature

The nisin-lipid II complex reveals a pyrophosphate cage that provides a blueprint for novel antibiotics.

Hsu, S.T.Breukink, E.Tischenko, E.Lutters, M.A.de Kruijff, B.Kaptein, R.Bonvin, A.M.van Nuland, N.A.

(2004) Nat Struct Mol Biol 11: 963-967

  • DOI: 10.1038/nsmb830
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The emerging antibiotics-resistance problem has underlined the urgent need for novel antimicrobial agents. Lantibiotics (lanthionine-containing antibiotics) are promising candidates to alleviate this problem. Nisin, a member of this family, has a uni ...

    The emerging antibiotics-resistance problem has underlined the urgent need for novel antimicrobial agents. Lantibiotics (lanthionine-containing antibiotics) are promising candidates to alleviate this problem. Nisin, a member of this family, has a unique pore-forming activity against bacteria. It binds to lipid II, the essential precursor of cell wall synthesis. As a result, the membrane permeabilization activity of nisin is increased by three orders of magnitude. Here we report the solution structure of the complex of nisin and lipid II. The structure shows a novel lipid II-binding motif in which the pyrophosphate moiety of lipid II is primarily coordinated by the N-terminal backbone amides of nisin via intermolecular hydrogen bonds. This cage structure provides a rationale for the conservation of the lanthionine rings among several lipid II-binding lantibiotics. The structure of the pyrophosphate cage offers a template for structure-based design of novel antibiotics.


    Related Citations: 
    • Mapping the Targeted Membrane Pore Formation Mechanism by Solution NMR: The Nisin Z and Lipid II Interaction in Sds Micelles
      Hsu, S.-T.D., Breukink, E., de Kruijff, B., Kaptein, R., Bonvin, A.M.J.J., van Nuland, N.A.J.
      (2002) Biochemistry 41: 7670
    • Use of the Cell Wall Precursor Lipid II by a Pore- Forming Peptide Antibiotic
      Breukink, E., Wiedemann, I., van Kraaij, C., Kuipers, O.P., Sahl, H.G., de Kruijff, B.
      (1999) Science 286: 2361
    • Refinement of Protein Structures in Explicit Solvent
      Linge, J., Williams, M.A., Spronk, C.A.E.M., Bonvin, A.M.J.J., Nilges, M.
      (2003) Proteins 50: 496
    • Haddock: A Protein-Protein Docking Approach Based on Biochemical or Biophysical Information
      Dominguez, C., Boelens, R., Bonvin, A.M.J.J.
      (2003) J Am Chem Soc 125: 1731

    Organizational Affiliation

    Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NISIN Z
N
34Lactococcus lactisMutation(s): 0 
Find proteins for P29559 (Lactococcus lactis subsp. lactis)
Go to UniProtKB:  P29559
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAG-MUB-ALA-FGA-LYS-DAL-DAL PEPTIDE
L
7Monarthropalpus flavusMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FPP
Query on FPP

Download CCD File 
N
FARNESYL DIPHOSPHATE
C15 H28 O7 P2
VWFJDQUYCIWHTN-YFVJMOTDSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000200
Query on PRD_000200
NNisin APolypeptide /  Lantibiotic

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Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
DBU
Query on DBU
NPEPTIDE LINKINGC4 H7 N O2THR
DHA
Query on DHA
NPEPTIDE LINKINGC3 H5 N O2SER
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: RMSD CLUSTERING AND LOWEST TOTAL ENERGY 
  • OLDERADO: 1WCO Olderado

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-03-07
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Structure summary, Version format compliance
  • Version 1.2: 2012-11-30
    Changes: Other
  • Version 2.0: 2018-01-17
    Changes: Advisory, Atomic model, Data collection, Database references