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 5.0 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: https://doi.org/10.1038/nsmb830
  • Primary Citation of Related Structures:  
    1WCO

  • 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 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.


  • Organizational Affiliation

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


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ALA-FGA-LYS-DAL-DAL PEPTIDEA [auth L]5Monarthropalpus flavusMutation(s): 0 
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
LantibioticB [auth N]34Lactococcus lactisMutation(s): 0 
UniProt
Find proteins for P29559 (Lactococcus lactis subsp. lactis)
Explore P29559 
Go to UniProtKB:  P29559
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29559
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-alpha-muramic acidC [auth A]2N/A
Glycosylation Resources
GlyTouCan:  G88499BX
GlyCosmos:  G88499BX
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FDF
Query on FDF

Download Ideal Coordinates CCD File 
D [auth L](2E,6E)-12-fluoro-11-(fluoromethyl)-3,7-dimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate
C15 H26 F2 O7 P2
PVNRGYDHHSWPHV-HJAIQHMZSA-N
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
DBU
Query on DBU
B [auth N]PEPTIDE LINKINGC4 H7 N O2THR
DHA
Query on DHA
B [auth N]PEPTIDE LINKINGC3 H5 N O2SER
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChains NameType/Class2D Diagram3D Interactions
PRD_000200
Query on PRD_000200
B [auth N]Nisin APolypeptide / Lantibiotic
Experimental Data & Validation

Experimental Data

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

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 3.0: 2020-07-08
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Source and taxonomy, Structure summary
  • Version 4.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 5.0: 2024-05-01
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Structure summary