4CL6

Crystal Structure of 3-hydroxydecanoyl-Acyl Carrier Protein Dehydratase (FabA) from Pseudomonas aeruginosa in complex with N-(4- Chlorobenzyl)-3-(2-furyl)-1H-1,2,4-triazol-5-amine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

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This is version 1.4 of the entry. See complete history


Literature

A Substrate Mimic Allows High Throughput Assay of the Faba Protein and Consequently the Identification of a Novel Inhibitor of Pseudomonas Aeruginosa Faba.

Moynie, L.Hope, A.G.Finzel, K.Schmidberger, J.Leckie, S.M.Schneider, G.Burkart, M.D.Smith, A.D.Gray, D.W.Naismith, J.H.

(2016) J Mol Biol 428: 108-120

  • DOI: 10.1016/j.jmb.2015.10.027
  • Primary Citation of Related Structures:  
    4CL6

  • PubMed Abstract: 
  • Eukaryotes and prokaryotes possess fatty acid synthase (FAS) biosynthetic pathways that comprise iterative chain elongation, reduction, and dehydration reactions. The bacterial FASII pathway differs significantly from human FAS pathways and is a long-standing target for antibiotic development against Gram-negative bacteria due to differences from the human FAS, and several existing antibacterial agents are known to inhibit FASII enzymes ...

    Eukaryotes and prokaryotes possess fatty acid synthase (FAS) biosynthetic pathways that comprise iterative chain elongation, reduction, and dehydration reactions. The bacterial FASII pathway differs significantly from human FAS pathways and is a long-standing target for antibiotic development against Gram-negative bacteria due to differences from the human FAS, and several existing antibacterial agents are known to inhibit FASII enzymes. N-Acetylcysteamine (NAC) fatty acid thioesters have been used as mimics of the natural acyl carrier protein pathway intermediates to assay FASII enzymes, and we now report an assay of FabV from Pseudomonas aeruginosa using (E)-2-decenoyl-NAC. In addition, we have converted an existing UV absorbance assay for FabA, the bifunctional dehydration/epimerization enzyme and key target in the FASII pathway, into a high-throughput enzyme coupled fluorescence assay that has been employed to screen a library of diverse small molecules. With this approach, N-(4-chlorobenzyl)-3-(2-furyl)-1H-1,2,4-triazol-5-amine (N42FTA) was found to competitively inhibit (pIC50=5.7±0.2) the processing of 3-hydroxydecanoyl-NAC by P. aeruginosa FabA. N42FTA was shown to be potent in blocking crosslinking of Escherichia coli acyl carrier protein and FabA, a direct mimic of the biological process. The co-complex structure of N42FTA with P. aeruginosa FabA protein rationalises affinity and suggests future design opportunities. Employing NAC fatty acid mimics to develop further high-throughput assays for individual enzymes in the FASII pathway should aid in the discovery of new antimicrobials.


    Organizational Affiliation

    Biomedical Sciences Research Complex and EaStCHEM, School of Chemistry, University of St. Andrews, North Haugh, St. Andrews, Fife KY16 9ST, United Kingdom; State Key Laboratory of Biotherapy, Sichuan University, Chengdu, Sichuan, China 610065. Electronic address: naismith@st-andrew.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASEA, B, C, D, E171Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: fabAPA1610
EC: 4.2.1.59 (PDB Primary Data), 5.3.3.14 (PDB Primary Data), 4.2.1.60 (PDB Primary Data)
UniProt
Find proteins for O33877 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore O33877 
Go to UniProtKB:  O33877
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7SB (Subject of Investigation/LOI)
Query on 7SB

Download Ideal Coordinates CCD File 
F [auth A], G [auth B], H [auth C], I [auth D], J [auth E]N-(4-chlorobenzyl)-5-(furan-2-yl)-1H-1,2,4-triazol-3-amine
C13 H11 Cl N4 O
IRHUOSKJHRHZKH-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
7SB Binding MOAD:  4CL6 Ka: 2.47e+5 (M^-1) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.61α = 90
b = 142.87β = 116.47
c = 77.85γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-21
    Type: Initial release
  • Version 1.1: 2015-11-18
    Changes: Database references
  • Version 1.2: 2015-11-25
    Changes: Database references
  • Version 1.3: 2016-03-02
    Changes: Database references
  • Version 1.4: 2018-06-13
    Changes: Data collection, Database references