4D46

Crystal structure of E. coli FabI in complex with NAD and 5-bromo-2-(4-chloro-2-hydroxyphenoxy)benzonitrile


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

An Ordered Water Channel in Staphylococcus Aureus Fabi: Unraveling the Mechanism of Substrate Recognition and Reduction.

Schiebel, J.Chang, A.Merget, B.Bommineni, G.R.Yu, W.Spagnuolo, L.A.Baxter, M.V.Tareilus, M.Tonge, P.J.Kisker, C.Sotriffer, C.A.

(2015) Biochemistry 54: 1943

  • DOI: 10.1021/bi5014358
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • One third of all drugs in clinical use owe their pharmacological activity to the functional inhibition of enzymes, highlighting the importance of enzymatic targets for drug development. Because of the close relationship between inhibition and catalys ...

    One third of all drugs in clinical use owe their pharmacological activity to the functional inhibition of enzymes, highlighting the importance of enzymatic targets for drug development. Because of the close relationship between inhibition and catalysis, understanding the recognition and turnover of enzymatic substrates is essential for rational drug design. Although the Staphylococcus aureus enoyl-acyl carrier protein reductase (saFabI) involved in bacterial fatty acid biosynthesis constitutes a very promising target for the development of novel, urgently needed anti-staphylococcal agents, the substrate binding mode and catalytic mechanism remained unclear for this enzyme. Using a combined crystallographic, kinetic, and computational approach, we have explored the chemical properties of the saFabI binding cavity, obtaining a consistent mechanistic model for substrate binding and turnover. We identified a water-molecule network linking the active site with a water basin inside the homo-tetrameric protein, which seems to be crucial for the closure of the flexible substrate binding loop as well as for an effective hydride and proton transfer during catalysis. On the basis of our results, we also derive a new model for the FabI-ACP complex that reveals how the ACP-bound acyl-substrate is injected into the FabI binding crevice. These findings support the future development of novel FabI inhibitors that target the FabI-ACP interface leading to the disruption of the interaction between these two proteins.


    Organizational Affiliation

    †Institute of Pharmacy and Food Chemistry, University of Wuerzburg, Am Hubland, D-97074 Wuerzburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]
A, B
270Escherichia coli (strain B / BL21-DE3)Mutation(s): 0 
EC: 1.3.1.9
Find proteins for A0A140NA83 (Escherichia coli (strain B / BL21-DE3))
Go to UniProtKB:  A0A140NA83
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download SDF File 
Download CCD File 
A, B
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
 Ligand Interaction
J47
Query on J47

Download SDF File 
Download CCD File 
A, B
5-bromo-2-(4-chloro-2-hydroxyphenoxy)benzonitrile
C13 H7 Br Cl N O2
FSWFNCWMADYOIM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.166 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 79.144α = 90.00
b = 79.144β = 90.00
c = 322.316γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-04
    Type: Initial release
  • Version 1.1: 2015-04-15
    Type: Database references