2WZV | pdb_00002wzv

Crystal structure of the FMN-dependent nitroreductase NfnB from Mycobacterium smegmatis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.174 (Depositor), 0.161 (DCC) 
  • R-Value Work: 
    0.151 (Depositor) 
  • R-Value Observed: 
    0.152 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Biological and Structural Characterization of the Mycobacterium Smegmatis Nitroreductase Nfnb, and its Role in Benzothiazinone Resistance

Manina, G.Bellinzoni, M.Pasca, M.R.Neres, J.Milano, A.Ribeiro, A.L.Buroni, S.Skovierova, H.Dianiskova, P.Mikusova, K.Marak, J.Makarov, V.Giganti, D.Haouz, A.Lucarelli, A.P.Degiacomi, G.Piazza, A.Chiarelli, L.R.De Rossi, E.Salina, E.Cole, S.T.Alzari, P.M.Riccardi, G.

(2010) Mol Microbiol 77: 1172

  • DOI: https://doi.org/10.1111/j.1365-2958.2010.07277.x
  • Primary Citation Related Structures: 
    2WZV, 2WZW

  • PubMed Abstract: 

    Tuberculosis is still a leading cause of death in developing countries, for which there is an urgent need for new pharmacological agents. The synthesis of the novel antimycobacterial drug class of benzothiazinones (BTZs) and the identification of their cellular target as DprE1 (Rv3790), a component of the decaprenylphosphoryl-β-d-ribose 2'-epimerase complex, have been reported recently. Here, we describe the identification and characterization of a novel resistance mechanism to BTZ in Mycobacterium smegmatis. The overexpression of the nitroreductase NfnB leads to the inactivation of the drug by reduction of a critical nitro-group to an amino-group. The direct involvement of NfnB in the inactivation of the lead compound BTZ043 was demonstrated by enzymology, microbiological assays and gene knockout experiments. We also report the crystal structure of NfnB in complex with the essential cofactor flavin mononucleotide, and show that a common amino acid stretch between NfnB and DprE1 is likely to be essential for the interaction with BTZ. We performed docking analysis of NfnB-BTZ in order to understand their interaction and the mechanism of nitroreduction. Although Mycobacterium tuberculosis seems to lack nitroreductases able to inactivate these drugs, our findings are valuable for the design of new BTZ molecules, which may be more effective in vivo.


  • Organizational Affiliation
    • Dipartimento di Genetica e Microbiologia, Università degli Studi di Pavia, via Ferrata, 1, 27100 Pavia, Italy.

Macromolecule Content 

  • Total Structure Weight: 53.35 kDa 
  • Atom Count: 3,933 
  • Modeled Residue Count: 445 
  • Deposited Residue Count: 470 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
NFNB PROTEIN
A, B
235Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
EC: 1
UniProt
Find proteins for A0R6D0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R6D0 
Go to UniProtKB:  A0R6D0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R6D0
Sequence Annotations
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Reference Sequence

Small Molecules

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

Query on FMN



Download:Ideal Coordinates CCD File
C [auth A],
G [auth B]
FLAVIN MONONUCLEOTIDE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
D [auth A],
H [auth B],
I [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A],
F [auth A],
J [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.174 (Depositor), 0.161 (DCC) 
  • R-Value Work:  0.151 (Depositor) 
  • R-Value Observed: 0.152 (Depositor) 
Space Group: I 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.19α = 90
b = 114.971β = 90
c = 118.901γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
SHELX-AUTOSHARPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-07-14
    Type: Initial release
  • Version 1.1: 2011-05-12
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Other, Structure summary