4JB6

Structure of Pseudomonas aeruginosa FabF mutant C164Q


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of Pseudomonas aeruginosa beta-ketoacyl-(acyl-carrier-protein) synthase II (FabF) and a C164Q mutant provide templates for antibacterial drug discovery and identify a buried potassium ion and a ligand-binding site that is an artefact of the crystal form.

Baum, B.Lecker, L.S.Zoltner, M.Jaenicke, E.Schnell, R.Hunter, W.N.Brenk, R.

(2015) Acta Crystallogr F Struct Biol Commun 71: 1020-1026

  • DOI: 10.1107/S2053230X15010614
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacterial infections remain a serious health concern, in particular causing life-threatening infections of hospitalized and immunocompromised patients. The situation is exacerbated by the rise in antibacterial drug resistance, and new treatments are ...

    Bacterial infections remain a serious health concern, in particular causing life-threatening infections of hospitalized and immunocompromised patients. The situation is exacerbated by the rise in antibacterial drug resistance, and new treatments are urgently sought. In this endeavour, accurate structures of molecular targets can support early-stage drug discovery. Here, crystal structures, in three distinct forms, of recombinant Pseudomonas aeruginosa β-ketoacyl-(acyl-carrier-protein) synthase II (FabF) are presented. This enzyme, which is involved in fatty-acid biosynthesis, has been validated by genetic and chemical means as an antibiotic target in Gram-positive bacteria and represents a potential target in Gram-negative bacteria. The structures of apo FabF, of a C164Q mutant in which the binding site is altered to resemble the substrate-bound state and of a complex with 3-(benzoylamino)-2-hydroxybenzoic acid are reported. This compound mimics aspects of a known natural product inhibitor, platensimycin, and surprisingly was observed binding outside the active site, interacting with a symmetry-related molecule. An unusual feature is a completely buried potassium-binding site that was identified in all three structures. Comparisons suggest that this may represent a conserved structural feature of FabF relevant to fold stability. The new structures provide templates for structure-based ligand design and, together with the protocols and reagents, may underpin a target-based drug-discovery project for urgently needed antibacterials.


    Organizational Affiliation

    Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität, Staudinger Weg 5, 55128 Mainz, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3-oxoacyl-[acyl-carrier-protein] synthase 2
A, B
414Pseudomonas aeruginosaMutation(s): 1 
Gene Names: fabF (fabF_1)
EC: 2.3.1.179
Find proteins for O54440 (Pseudomonas aeruginosa)
Go to UniProtKB:  O54440
Small Molecules
Ligands 1 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.179 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 101.073α = 90.00
b = 104.619β = 90.00
c = 141.601γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2013-02-19 
  • Released Date: 2014-03-05 
  • Deposition Author(s): Baum, B., Lecker, L.

Revision History 

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2015-08-12
    Type: Database references
  • Version 1.2: 2015-08-26
    Type: Database references