4LS7

Crystal structure of Bacillus subtilis beta-ketoacyl-ACP synthase II (FabF) in a non-covalent complex with cerulenin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.674 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.151 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural insights into bacterial resistance to cerulenin.

Trajtenberg, F.Altabe, S.Larrieux, N.Ficarra, F.de Mendoza, D.Buschiazzo, A.Schujman, G.E.

(2014) Febs J. 281: 2324-2338

  • DOI: 10.1111/febs.12785
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cerulenin is a fungal toxin that inhibits both eukaryotic and prokaryotic ketoacyl-acyl carrier protein synthases or condensing enzymes. It has been used experimentally to treat cancer and obesity, and is a potent inhibitor of bacterial growth. Under ...

    Cerulenin is a fungal toxin that inhibits both eukaryotic and prokaryotic ketoacyl-acyl carrier protein synthases or condensing enzymes. It has been used experimentally to treat cancer and obesity, and is a potent inhibitor of bacterial growth. Understanding the molecular mechanisms of resistance to cerulenin and similar compounds is thus highly relevant for human health. We have previously described a Bacillus subtilis cerulenin-resistant strain, expressing a point-mutated condensing enzyme FabF (FabF[I108F]) (i.e. FabF with isoleucine 108 substituted by phenylalanine). We now report the crystal structures of wild-type FabF from B. subtilis, both alone and in complex with cerulenin, as well as of the FabF[I108F] mutant protein. The three-dimensional structure of FabF[I108F] constitutes the first atomic model of a condensing enzyme that remains active in the presence of the inhibitor. Soaking the mycotoxin into preformed wild-type FabF crystals allowed for noncovalent binding into its specific pocket within the FabF core. Interestingly, only co-crystallization experiments allowed us to trap the covalent complex. Our structure shows that the covalent bond between Cys163 and cerulenin, in contrast to that previously proposed, implicates carbon C3 of the inhibitor. The similarities between Escherichia coli and B. subtilis FabF structures did not explain the reported inability of ecFabF[I108F] (i.e. FabF from Escherichia coli with isoleucine 108 substituted by phenylalanine) to elongate medium and long-chain acyl-ACPs. We now demonstrate that the E. coli modified enzyme efficiently catalyzes the synthesis of medium and long-chain ketoacyl-ACPs. We also characterized another cerulenin-insensitive form of FabF, conferring a different phenotype in B. subtilis. The structural, biochemical and physiological data presented, shed light on the mechanisms of FabF catalysis and resistance to cerulenin.


    Organizational Affiliation

    Institut Pasteur de Montevideo, Unit of Protein Crystallography, Montevideo, Uruguay.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-oxoacyl-[acyl-carrier-protein] synthase 2
A, B
426Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: fabF (yjaY)
EC: 2.3.1.179
Find proteins for O34340 (Bacillus subtilis (strain 168))
Go to UniProtKB:  O34340
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
1X9
Query on 1X9

Download SDF File 
Download CCD File 
A, B
Cerulenin
(2R,3S)-3-[(4E,7E)-nona-4,7-dienoyl]oxirane-2-carboxamide
C12 H17 N O3
GVEZIHKRYBHEFX-NQQPLRFYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.674 Å
  • R-Value Free: 0.180 
  • R-Value Work: 0.151 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 72.266α = 90.00
b = 87.721β = 90.00
c = 144.730γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PDB_EXTRACTdata extraction
SCALAdata scaling
PHENIXrefinement
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-04-02
    Type: Initial release
  • Version 1.1: 2014-06-04
    Type: Database references