Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 98.24 kDa 
• Atom Count: 7307 
• Residue Count: 864 
• Unique protein chains: 1

1KQB

Structure of Nitroreductase from E. cloacae complex with inhibitor benzoate

• DOI: 10.2210/pdb1KQB/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Enterobacter cloacae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2002-01-04 Released: 2002-02-13 
• Deposition Author(s): Haynes, C.A., Koder, R.L., Miller, A.F., Rodgers, D.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.217 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 

Literature

Structures of nitroreductase in three states: effects of inhibitor binding and reduction.

Haynes, C.A., Koder, R.L., Miller, A.F., Rodgers, D.W.

(2002) J Biol Chem 277: 11513-11520

• PubMed: 11805110 
• DOI: 10.1074/jbc.M111334200
• Primary Citation of Related Structures:  
  1KQD, 1KQC, 1KQB


• PubMed Abstract: 
  

The crystal structure of the nitroreductase enzyme from Enterobacter cloacae has been determined for the oxidized form in separate complexes with benzoate and acetate inhibitors and for the two-electron reduced form. Nitroreductase is a member of a group of enzymes that reduce a broad range of nitroaromatic compounds and has potential uses in chemotherapy and bioremediation. The monomers of the nitroreductase dimer adopt an alpha+beta fold and together bind two flavin mononucleotide prosthetic groups at the dimer interface. In the oxidized enzyme, the flavin ring system adopts a strongly bent (16 degrees ) conformation, and the bend increases (25 degrees ) in the reduced form of the enzyme, roughly the conformation predicted for reduced flavin free in solution. Because free oxidized flavin is planar, the induced bend in the oxidized enzyme may favor reduction, and it may also account for the characteristic inability of the enzyme to stabilize the one electron-reduced semiquinone flavin, which is also planar. Both inhibitors bind over the pyrimidine and central rings of the flavin in partially overlapping sites. Comparison of the two inhibitor complexes shows that a portion of helix H6 can flex to accommodate the differently sized inhibitors suggesting a mechanism for accommodating varied substrates.

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Organizational Affiliation: 

Department of Molecular and Cellular Biochemistry, The University of Kentucky, Lexington, Kentucky 40536, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
OXYGEN-INSENSITIVE NAD(P)H NITROREDUCTASE	A, B, C, D	217	Enterobacter cloacae	Mutation(s): 0  Gene Names: nfsB, nfnB, nfsI EC: 1.6.6 (PDB Primary Data), 1 (UniProt)
Find proteins for Q01234 (Enterobacter cloacae) Explore Q01234  Go to UniProtKB:  Q01234

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	A, B, C, D	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
BEZ	A, B, C, D	BENZOIC ACID C7 H6 O2 WPYMKLBDIGXBTP-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
BEZ	Ki:  100000   nM  Binding MOAD
BEZ	Ki :  100000   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.217 
• R-Value Work: 0.188 
• R-Value Observed: 0.190 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.84	α = 90
b = 79.31	β = 93.69
c = 96.92	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-01-04 
• Released Date: 2002-02-13 
Deposition Author(s): Haynes, C.A., Koder, R.L., Miller, A.F., Rodgers, D.W.

Revision History 

• Version 1.0: 2002-02-13
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description