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

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

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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: https://doi.org/10.1074/jbc.M114.629485
  • Primary Citation of Related Structures:  

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D
429Nocardia farcinica IFM 10152Mutation(s): 1 
Find proteins for Q5Z1T5 (Nocardia farcinica (strain IFM 10152))
Explore Q5Z1T5 
Go to UniProtKB:  Q5Z1T5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5Z1T5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.64α = 90
b = 121.92β = 97.72
c = 91.86γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-01
    Type: Initial release
  • Version 1.1: 2015-04-08
    Changes: Database references
  • Version 1.2: 2015-06-03
    Changes: Database references
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other