5HEI | pdb_00005hei

Structure of B. megaterium NfrA2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 
    0.247 (Depositor), 0.300 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.251 (DCC) 
  • R-Value Observed: 
    0.205 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5HEI

Ligand Structure Quality Assessment 


This is version 1.2 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: https://doi.org/10.1042/BJ20151366
  • Primary Citation 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 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.

Macromolecule Content 

  • Total Structure Weight: 229.14 kDa 
  • Atom Count: 15,833 
  • Modeled Residue Count: 1,967 
  • Deposited Residue Count: 2,024 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NfrA2
A, B, C, D, E
A, B, C, D, E, F, G, H
253Priestia megateriumMutation(s): 0 
Gene Names: nfrA2
EC: 1.5.1.38
UniProt
Find proteins for A0A0K0VJM8 (Priestia megaterium)
Explore A0A0K0VJM8 
Go to UniProtKB:  A0A0K0VJM8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0K0VJM8
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FMN

Query on FMN



Download:Ideal Coordinates CCD File
I [auth A]
J [auth B]
K [auth C]
N [auth D]
Q [auth E]
I [auth A],
J [auth B],
K [auth C],
N [auth D],
Q [auth E],
R [auth F],
S [auth G],
U [auth H]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
MPD

Query on MPD



Download:Ideal Coordinates CCD File
L [auth C],
V [auth H]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
M [auth C],
O [auth D],
P [auth D],
T [auth G],
W [auth H]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free:  0.247 (Depositor), 0.300 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.251 (DCC) 
  • R-Value Observed: 0.205 (Depositor) 
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

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-06
    Type: Initial release
  • Version 1.1: 2016-06-01
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description