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


This is version 2.0 of the entry. See complete history

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
  • Also Cited By: 1W9N

  • 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: 
    • 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
    • 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
    • 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: Struct.,Funct., Genet. 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: 1
MoleculeChainsSequence LengthOrganismDetails
NAG-MUB-ALA-FGA-LYS-DAL-DAL PEPTIDE
L
7N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NISIN Z
N
34Lactococcus lactis subsp. lactisGene Names: nisZ
Find proteins for P29559 (Lactococcus lactis subsp. lactis)
Go to UniProtKB:  P29559
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FPP
Query on FPP

Download SDF File 
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  3 Unique
IDChainsTypeFormula2D DiagramParent
MUB
Query on MUB
L
NON-POLYMERC11 H19 N O8

--

FGA
Query on FGA
L
D-gamma-peptide, C-delta linkingC5 H9 N O4

--

NAG
Query on NAG
L
D-SACCHARIDEC8 H15 N O6

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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 or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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