Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.19 kDa 
• Atom Count: 1557 
• Modelled Residue Count: 174 
• Deposited Residue Count: 200 
• Unique protein chains: 1

3D3H

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

• PDB DOI: 10.2210/pdb3D3H/pdb

• Classification: TRANSFERASE/ANTIBIOTIC
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-05-11 Released: 2008-07-22 
• Deposition Author(s): Yuan, Y., Sliz, P., Walker, S.

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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 

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

• PubMed: 18642800 
• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Penicillin-insensitive transglycosylase	A	200	Aquifex aeolicus	Mutation(s): 0  Gene Names: mrcA, ponA 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M4O	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

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 = 54.939	α = 90
b = 100.448	β = 90
c = 104.022	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-05-11 
• Released Date: 2008-07-22 
Deposition Author(s): Yuan, Y., Sliz, P., Walker, S.

Revision History  

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