4D43

Crystal structure of S. aureus FabI in complex with NADP and 2-(2- chloro-4-nitrophenoxy)-5-ethyl-4-fluorophenol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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:  
    4D44, 4D45, 4D46, 4D41, 4D42, 4D43

  • 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 catalysis, understanding the recognition and turnover of enzymatic substrates is essential for rational drug design ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]A, B, C, D, E, F, G, H282Staphylococcus aureus subsp. aureus N315Mutation(s): 1 
EC: 1.3.1.10 (PDB Primary Data), 1.3.1.39 (UniProt)
UniProt
Find proteins for A0A0J9X1Y0 (Staphylococcus aureus (strain N315))
Explore A0A0J9X1Y0 
Go to UniProtKB:  A0A0J9X1Y0
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
DA [auth F], IA [auth G], K [auth A], KA [auth H], O [auth B], S [auth C], U [auth D], Z [auth E]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
9W7 (Subject of Investigation/LOI)
Query on 9W7

Download Ideal Coordinates CCD File 
AA [auth E], EA [auth F], JA [auth G], L [auth A], MA [auth H], P [auth B], T [auth C], V [auth D]2-(2-chloro-4-nitrophenoxy)-5-ethyl-4-fluorophenol
C14 H11 Cl F N O4
RGNGXGXBSAFDJR-UHFFFAOYSA-N
 Ligand Interaction
GLU
Query on GLU

Download Ideal Coordinates CCD File 
BA [auth F], FA [auth G], I [auth A], M [auth B], Q [auth C], X [auth E]GLUTAMIC ACID
C5 H9 N O4
WHUUTDBJXJRKMK-VKHMYHEASA-N
 Ligand Interaction
MRD
Query on MRD

Download Ideal Coordinates CCD File 
CA [auth F] , GA [auth G] , HA [auth G] , J [auth A] , LA [auth H] , N [auth B] , R [auth C] , W [auth D] , 
CA [auth F],  GA [auth G],  HA [auth G],  J [auth A],  LA [auth H],  N [auth B],  R [auth C],  W [auth D],  Y [auth E]
(4R)-2-METHYLPENTANE-2,4-DIOL
C6 H14 O2
SVTBMSDMJJWYQN-RXMQYKEDSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
9W7 Binding MOAD:  4D43 Ki: 0.75 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.173 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.18α = 98.45
b = 94.88β = 111.49
c = 94.9γ = 97.3
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

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