1DFI

X-RAY STRUCTURE OF ESCHERICHIA COLI ENOYL REDUCTASE WITH BOUND NAD

• PDB DOI: https://doi.org/10.2210/pdb1DFI/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 1997-01-16 Released: 1998-01-28 
• Deposition Author(s): Baldock, C., Rafferty, J.B., Rice, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Work: 0.162 

Starting Model: experimental

Literature

A mechanism of drug action revealed by structural studies of enoyl reductase.

Baldock, C., Rafferty, J.B., Sedelnikova, S.E., Baker, P.J., Stuitje, A.R., Slabas, A.R., Hawkes, T.R., Rice, D.W.

(1996) Science 274: 2107-2110

• PubMed: 8953047 
• DOI: https://doi.org/10.1126/science.274.5295.2107
• Primary Citation of Related Structures:  
  1DFG, 1DFH, 1DFI


• PubMed Abstract: 
  

  Enoyl reductase (ENR), an enzyme involved in fatty acid biosynthesis, is the target for antibacterial diazaborines and the front-line antituberculosis drug isoniazid. Analysis of the structures of complexes of Escherichia coli ENR with nicotinamide adenine dinucleotide and either thienodiazaborine or benzodiazaborine revealed the formation of a covalent bond between the 2' hydroxyl of the nicotinamide ribose and a boron atom in the drugs to generate a tight, noncovalently bound bisubstrate analog. This analysis has implications for the structure-based design of inhibitors of ENR, and similarities to other oxidoreductases suggest that mimicking this molecular linkage may have generic applications in other areas of medicinal chemistry.

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Organizational Affiliation: 

Krebs Institute for Biomolecular Research, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, UK. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 113.7 kDa 
• Atom Count: 7,839 
• Modelled Residue Count: 988 
• Deposited Residue Count: 1,044 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ENOYL ACYL CARRIER PROTEIN REDUCTASE	A, B, C, D	261	Escherichia coli	Mutation(s): 0  EC: 1.3.1.9
UniProt
Find proteins for P0AEK4 (Escherichia coli (strain K12)) Explore P0AEK4  Go to UniProtKB:  P0AEK4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], F [auth B], G [auth C], H [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.09 Å
• R-Value Work: 0.162 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74	α = 90
b = 81.2	β = 92.9
c = 79	γ = 90

Software Package:

Software Name	Purpose
CCP4	model building
TNT	refinement
MOSFLM	data reduction
Agrovata	data scaling
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-01-28 
Deposition Author(s): Baldock, C., Rafferty, J.B., Rice, D.W.

Revision History  

• Version 1.0: 1998-01-28
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-09
  Changes: Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-05-22
  Changes: Data collection