4AG3

Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG) from Pseudomonas aeruginosa in complex with NADPH at 1.8A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery of an Allosteric Inhibitor Binding Site in 3-Oxo-Acyl-Acp Reductase from Pseudomonas Aeruginosa

Cukier, C.D.Hope, A.Elamin, A.Moynie, L.Schnell, R.Schach, S.Kneuper, H.Singh, M.Naismith, J.Lindqvist, Y.Gray, D.Schneider, G.

(2013) ACS Chem Biol 8: 2518

  • DOI: 10.1021/cb4005063
  • Primary Citation of Related Structures:  
    4BNX, 4BO9, 4BNY, 4BNZ, 4BO1, 4BO2, 4BO3, 4BO4, 4BNT, 4BO5

  • PubMed Abstract: 
  • 3-Oxo-acyl-acyl carrier protein (ACP) reductase (FabG) plays a key role in the bacterial fatty acid synthesis II system in pathogenic microorganisms, which has been recognized as a potential drug target. FabG catalyzes reduction of a 3-oxo-acyl-ACP intermediate during the elongation cycle of fatty acid biosynthesis ...

    3-Oxo-acyl-acyl carrier protein (ACP) reductase (FabG) plays a key role in the bacterial fatty acid synthesis II system in pathogenic microorganisms, which has been recognized as a potential drug target. FabG catalyzes reduction of a 3-oxo-acyl-ACP intermediate during the elongation cycle of fatty acid biosynthesis. Here, we report gene deletion experiments that support the essentiality of this gene in P. aeruginosa and the identification of a number of small molecule FabG inhibitors with IC50 values in the nanomolar to low micromolar range and good physicochemical properties. Structural characterization of 16 FabG-inhibitor complexes by X-ray crystallography revealed that the compounds bind at a novel allosteric site located at the FabG subunit-subunit interface. Inhibitor binding relies primarily on hydrophobic interactions, but specific hydrogen bonds are also observed. Importantly, the binding cavity is formed upon complex formation and therefore would not be recognized by virtual screening approaches. The structure analysis further reveals that the inhibitors act by inducing conformational changes that propagate to the active site, resulting in a displacement of the catalytic triad and the inability to bind NADPH.


    Related Citations: 
    • The Aeropath Project Targeting Pseudomonas Aeruginosa: Crystallographic Studies for Assessment of Potential Targets in Early-Stage Drug Discovery.
      Moynie, L., Schnell, R., Mcmahon, S.A., Sandalova, T., Boulkerou, W.A., Schmidberger, J.W., Alphey, M., Cukier, C., Duthie, F., Kopec, J., Liu, H., Jacewicz, A., Hunter, W.N., Naismith, J.H., Schneider, G.
      (2013) Acta Crystallogr Sect F Struct Biol Cryst Commun 69: 25

    Organizational Affiliation

    Department of Medical Biochemistry and Biophysics, Karolinska Institutet , 17177 Stockholm, Sweden.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-OXOACYL-[ACYL-CARRIER-PROTEIN] REDUCTASE FABGABCD269Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: fabGPA2967
EC: 1.1.1.100
Find proteins for O54438 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore O54438 
Go to UniProtKB:  O54438
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDP
Query on NDP

Download CCD File 
A, B, C
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H30 N7 O17 P3
ACFIXJIJDZMPPO-NNYOXOHSSA-N
 Ligand Interaction
1PE
Query on 1PE

Download CCD File 
A, B, C, D
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.160 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.2α = 90
b = 112.21β = 90
c = 116.98γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-02-06
    Type: Initial release
  • Version 1.1: 2013-09-18
    Changes: Database references
  • Version 1.2: 2013-11-27
    Changes: Database references