5HEI

Structure of B. megaterium NfrA2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Functional and structural characterization of two Bacillus megaterium nitroreductases biotransforming the herbicide mesotrione.

Carles, L.Besse-Hoggan, P.Joly, M.Vigouroux, A.Morera, S.Batisson, I.

(2016) Biochem J 473: 1443-1453

  • DOI: 10.1042/BJ20151366
  • Primary Citation of Related Structures:  
    5HDJ, 5HEI

  • PubMed Abstract: 
  • Mesotrione is a selective herbicide belonging to the triketone family, commonly used on maize cultures since 2003. A mesotrione-transforming Bacillus megaterium Mes11 strain isolated from an agricultural soil was used as a model to identify the key e ...

    Mesotrione is a selective herbicide belonging to the triketone family, commonly used on maize cultures since 2003. A mesotrione-transforming Bacillus megaterium Mes11 strain isolated from an agricultural soil was used as a model to identify the key enzymes initiating the biotransformation of this herbicide. Two enzymes (called NfrA1 and NfrA2/YcnD) were identified, and functionally and structurally characterized. Both belong to the NfsA FRP family of the nitro-FMN reductase superfamily (type I oxygen-insensitive nitroreductase) and show optimal pH and temperature of 6-6.5 and 23-25°C, respectively. Both undergo a Ping Pong Bi Bi mechanism, with NADPH and NADPH/NADH as cofactors for NfrA1 and NfrA2/YcnD, respectively. It is interesting that both can also reduce various nitro compounds including pesticides, antibiotics, one prodrug and 4-methylsulfonyl-2-nitrobenzoic acid, one of the mesotrione metabolites retrieved from the environment. The present study constitutes the first identification of mesotrione-transforming enzymes. These enzymes (or their corresponding genes) could be used as biomarkers to predict the capacity of ecosystems to transform mesotrione and assess their contamination by both the parent molecule and/or the metabolites.


    Organizational Affiliation

    Clermont Université, Université Blaise Pascal, Laboratoire Microorganismes: Génome et Environnement (LMGE), F-63000 Clermont-Ferrand, France Centre National de la Recherche Scientifique (CNRS), UMR 6023, LMGE, TSA 60026, CS 60026, 63178 Aubière Cedex, France isabelle.batisson@univ-bpclermont.fr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NfrA2ABCDEFGH253Bacillus megateriumMutation(s): 0 
Gene Names: nfrA2CN918_01570
Find proteins for A0A0K0VJM8 (Bacillus megaterium)
Explore A0A0K0VJM8 
Go to UniProtKB:  A0A0K0VJM8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMN
Query on FMN

Download CCD File 
A, B, C, D, E, F, G, H
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
MPD
Query on MPD

Download CCD File 
C, H
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
C, D, G, H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.44α = 90
b = 158.19β = 102.21
c = 103.86γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2016-06-01
    Changes: Database references