1AJ1

NMR STRUCTURE OF THE LANTIBIOTIC ACTAGARDINE


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 15 
  • Selection Criteria: LEAST RESTRAINT VIOLATIONS, BEST RELAXATION MATRIX R- FACTORS 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

The Three-Dimensional Solution Structure of the Lantibiotic Murein-Biosynthesis-Inhibitor Actagardine Determined by NMR.

Zimmermann, N.Jung, G.

(1997) Eur.J.Biochem. 246: 809


  • PubMed Abstract: 
  • The three-dimensional solution structure of the lantibiotic actagardine was determined at high resolution by homonuclear and heteronuclear two-dimensional and three-dimensional NMR spectroscopy in [2H3]acetonitrile/H2O (7:3). 133 non-trivial distance ...

    The three-dimensional solution structure of the lantibiotic actagardine was determined at high resolution by homonuclear and heteronuclear two-dimensional and three-dimensional NMR spectroscopy in [2H3]acetonitrile/H2O (7:3). 133 non-trivial distance and 22 torsional-angle constraints were derived from the NMR data. An ensemble of 15 low-energy structures was calculated by distance geometry followed by an iterative relaxation-matrix-refinement procedure. The rmsd of the backbone coordinates with respect to the average structure was 17 pm. The two distinct thioether ring systems 1-6 and 7-19 were even better defined, with backbone rmsd of 10 pm and 14 pm, respectively. Actagardine shows a rigid compact globular shape based on the constraining bridging pattern, which is composed of an N-terminal lanthionine ring from residues 1-6 and three intertwined C-terminal methyllanthionine rings comprising residues 7-12, 9-17 and 14-19. In addition, this C-terminal ring system is stabilised by a short antiparallel beta sheet. A feature of the actagardine structure is the presence of two putative binding pockets. A pocket is generated by the covalent constraints of the C-terminal thioether ring system. The rim of this pocket is built up by a loop structure comprising residues 12-19, whose backbone amide protons are all directed to the centre of the pocket. The second pocket is formed by an L-shaped orientation of the N-terminal and C-terminal thioether ring systems. The only two hydrophilic amino acid residues of actagardine, Glu11 and Ser2, are directed to this pocket. A region of high sequence similarity with the related lantibiotic mersacidin is located exactly at the position of the second pocket (residues 3-12). This suggests that the second pocket is responsible for the antibiotic mode of action of actagardine and mersacidin as inhibitors of the murein biosynthesis of gram-positive bacteria.


    Related Citations: 
    • The Tetracyclic Lantibiotic Actagardine. 1H-NMR and 13C-NMR Assignments and Revised Primary Structure
      Zimmermann, N.,Metzger, J.W.,Jung, G.
      (1995) Eur.J.Biochem. 228: 786


    Organizational Affiliation

    Institut für Organische Chemie, Universität Tübingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LANTIBIOTIC ACTAGARDINE
A
19Actinoplanes liguriensisMutation(s): 0 
Find proteins for P56650 (Actinoplanes liguriensis)
Go to UniProtKB:  P56650
Small Molecules
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000194
Query on PRD_000194
AACTAGARDINEOligopeptide / Lantibiotic

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Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 100 
  • Conformers Submitted: 15 
  • Selection Criteria: LEAST RESTRAINT VIOLATIONS, BEST RELAXATION MATRIX R- FACTORS 
  • Olderado: 1AJ1 Olderado

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-10-15
    Type: Initial release
  • Version 1.1: 2011-06-14
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2011-07-27
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
  • Version 1.4: 2012-12-12
    Type: Other