3D3H

Crystal structure of a complex of the peptidoglycan glycosyltransferase domain from Aquifex aeolicus and neryl moenomycin A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 

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This is version 1.1 of the entry. See complete history


Literature

Structural analysis of the contacts anchoring moenomycin to peptidoglycan glycosyltransferases and implications for antibiotic design.

Yuan, Y.Fuse, S.Ostash, B.Sliz, P.Kahne, D.Walker, S.

(2008) ACS Chem Biol 3: 429-436

  • DOI: 10.1021/cb800078a
  • Primary Citation of Related Structures:  
    3D3H

  • PubMed Abstract: 
  • Peptidoglycan glycosyltransferases (PGTs), enzymes that catalyze the formation of the glycan chains of the bacterial cell wall, have tremendous potential as antibiotic targets. The moenomycins, a potent family of natural product antibiotics, are the only known active site inhibitors of the PGTs and serve as blueprints for the structure-based design of new antibacterials ...

    Peptidoglycan glycosyltransferases (PGTs), enzymes that catalyze the formation of the glycan chains of the bacterial cell wall, have tremendous potential as antibiotic targets. The moenomycins, a potent family of natural product antibiotics, are the only known active site inhibitors of the PGTs and serve as blueprints for the structure-based design of new antibacterials. A 2.8 A structure of a Staphylococcus aureus PGT with moenomycin A bound in the active site appeared recently, potentially providing insight into substrate binding; however, the protein-ligand contacts were not analyzed in detail and the implications of the structure for inhibitor design were not addressed. We report here the 2.3 A structure of a complex of neryl-moenomycin A bound to the PGT domain of Aquifex aeolicus PBP1A. The structure allows us to examine protein-ligand contacts in detail and implies that six conserved active site residues contact the centrally located F-ring phosphoglycerate portion of neryl-moenomycin A. A mutational analysis shows that all six residues play important roles in enzymatic activity. We suggest that small scaffolds that maintain these key contacts will serve as effective PGT inhibitors. To test this hypothesis, we have prepared, via heterologous expression of a subset of moenomycin biosynthetic genes, a novel moenomycin intermediate that maintains these six contacts but does not contain the putative minimal pharmacophore. This compound has comparable biological activity to the previously proposed minimal pharmacophore. The results reported here may facilitate the design of antibiotics targeted against peptidoglycan glycosyltransferases.


    Organizational Affiliation

    Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Penicillin-insensitive transglycosylaseA200Aquifex aeolicusMutation(s): 0 
Gene Names: mrcAponA
EC: 2.4.2 (PDB Primary Data), 2.4.1.129 (UniProt), 3.4.16.4 (UniProt)
UniProt
Find proteins for O66874 (Aquifex aeolicus (strain VF5))
Explore O66874 
Go to UniProtKB:  O66874
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO66874
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
M4O
Query on M4O

Download Ideal Coordinates CCD File 
B [auth A](2R)-3-{[(S)-{[(2R,3R,4R,5S,6S)-3-{[(2S,3R,4R,5S,6R)-3-(acetylamino)-5-{[(2S,3R,4R,5S,6R)-3-(acetylamino)-5-{[(2R,3R,4S,5R,6S)-6-carbamoyl-3,4,5-trihydroxytetrahydro-2H-pyran-2-yl]oxy}-4-hydroxy-6-methyltetrahydro-2H-pyran-2-yl]oxy}-4-hydroxy-6-({[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]oxy}methyl)tetrahydro-2H-pyran-2-yl]oxy}-6-carbamoyl-4-(carbamoyloxy)-5-hydroxy-5-methyltetrahydro-2H-pyran-2-yl]oxy}(hydroxy)phosphoryl]oxy}-2-{[(2Z)-3,7-dimethylocta-2,6-dien-1-yl]oxy}propanoic acid
C49 H80 N5 O32 P
RAPYBPXXZJZLIC-LMVGRRJQSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.225 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.939α = 90
b = 100.448β = 90
c = 104.022γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Non-polymer description, Version format compliance