4D7E

An unprecedented NADPH domain conformation in Lysine Monooxygenase NbtG from Nocardia farcinica


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

An Unprecedented Nadph Domain Conformation in Lysine Monooxygenase Nbtg Provides Insights Into Uncoupling of Oxygen Consumption from Substrate Hydroxylation.

Binda, C.Robinson, R.M.Martin Del Campo, J.S.Keul, N.D.Rodriguez, P.J.Robinson, H.H.Mattevi, A.Sobrado, P.

(2015) J.Biol.Chem. 290: 12676

  • DOI: 10.1074/jbc.M114.629485

  • PubMed Abstract: 
  • N-Hydroxylating monooxygenases are involved in the biosynthesis of iron-chelating hydroxamate-containing siderophores that play a role in microbial virulence. These flavoenzymes catalyze the NADPH- and oxygen-dependent hydroxylation of amines such as ...

    N-Hydroxylating monooxygenases are involved in the biosynthesis of iron-chelating hydroxamate-containing siderophores that play a role in microbial virulence. These flavoenzymes catalyze the NADPH- and oxygen-dependent hydroxylation of amines such as those found on the side chains of lysine and ornithine. In this work we report the biochemical and structural characterization of Nocardia farcinica Lys monooxygenase (NbtG), which has similar biochemical properties to mycobacterial homologs. NbtG is also active on d-Lys, although it binds l-Lys with a higher affinity. Differently from the ornithine monooxygenases PvdA, SidA, and KtzI, NbtG can use both NADH and NADPH and is highly uncoupled, producing more superoxide and hydrogen peroxide than hydroxylated Lys. The crystal structure of NbtG solved at 2.4 Å resolution revealed an unexpected protein conformation with a 30° rotation of the NAD(P)H domain with respect to the flavin adenine dinucleotide (FAD) domain that precludes binding of the nicotinamide cofactor. This "occluded" structure may explain the biochemical properties of NbtG, specifically with regard to the substantial uncoupling and limited stabilization of the C4a-hydroperoxyflavin intermediate. Biological implications of these findings are discussed.


    Organizational Affiliation

    From the Department of Biology and Biotechnology, University of Pavia, Pavia 27100, Italy.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-LYS MONOOXYGENASE
A, B, C, D
429Nocardia farcinica (strain IFM 10152)Mutation(s): 1 
Gene Names: nbtG
Find proteins for Q5Z1T5 (Nocardia farcinica (strain IFM 10152))
Go to UniProtKB:  Q5Z1T5
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download SDF File 
Download CCD File 
A, B, C, D
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 80.640α = 90.00
b = 121.920β = 97.72
c = 91.860γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-04-01
    Type: Initial release
  • Version 1.1: 2015-04-08
    Type: Database references
  • Version 1.2: 2015-06-03
    Type: Database references