3N2S

Structure of NfrA1 nitroreductase from B. subtilis

• PDB DOI: https://doi.org/10.2210/pdb3N2S/pdb

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


• Deposited: 2010-05-19 Released: 2010-09-15 
• Deposition Author(s): Morera, S., Gueguen-Chaignon, V., Meyer, P., Cortial, S., Ouazzani, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.198 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 

Literature

NADH oxidase activity of Bacillus subtilis nitroreductase NfrA1: insight into its biological role.

Cortial, S., Chaignon, P., Iorga, B.I., Aymerich, S., Truan, G., Gueguen-Chaignon, V., Meyer, P., Morera, S., Ouazzani, J.

(2010) FEBS Lett 584: 3916-3922

• PubMed: 20727352 
• DOI: https://doi.org/10.1016/j.febslet.2010.08.019
• Primary Citation of Related Structures:  
  3N2S


• PubMed Abstract: 
  

  NfrA1 nitroreductase from the Gram-positive bacterium Bacillus subtilis is a member of the NAD(P)H/FMN oxidoreductase family. Here, we investigated the reactivity, the structure and kinetics of NfrA1, which could provide insight into the unclear biological role of this enzyme. We could show that NfrA1 possesses an NADH oxidase activity that leads to high concentrations of oxygen peroxide and an NAD(+) degrading activity leading to free nicotinamide. Finally, we showed that NfrA1 is able to rapidly scavenge H(2)O(2) produced during the oxidative process or added exogenously.

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Organizational Affiliation: 

Institut de Chimie des Substances Naturelles (ICSN), CNRS UPR 2301, Gif-sur-Yvette, France.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 116.63 kDa 
• Atom Count: 8,442 
• Modelled Residue Count: 991 
• Deposited Residue Count: 996 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NADPH-dependent nitro/flavin reductase	A, B, C, D	249	Bacillus subtilis	Mutation(s): 0  Gene Names: nfrA1, nfrA, ywcG, BSU38110, ipa-43d EC: 1.5.1.29
UniProt
Find proteins for P39605 (Bacillus subtilis (strain 168)) Explore P39605  Go to UniProtKB:  P39605

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMN	E [auth A], G [auth B], I [auth C], J [auth D]	FLAVIN MONONUCLEOTIDE C17 H21 N4 O9 P FVTCRASFADXXNN-SCRDCRAPSA-N
CL	F [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C, D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.198 
• R-Value Work: 0.173 
• R-Value Observed: 0.174 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.55	α = 87.68
b = 54.81	β = 87.64
c = 90.5	γ = 65.14

Software Package:

Software Name	Purpose
DNA	data collection
SHELXS	phasing
BUSTER	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-15 
Deposition Author(s): Morera, S., Gueguen-Chaignon, V., Meyer, P., Cortial, S., Ouazzani, J.

Revision History  

• Version 1.0: 2010-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance