5N2I

F420:NADPH oxidoreductase from Thermobifida fusca with NADP+ bound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Isolation and characterization of a thermostable F420:NADPH oxidoreductase from Thermobifida fusca.

Kumar, H.Nguyen, Q.T.Binda, C.Mattevi, A.Fraaije, M.W.

(2017) J Biol Chem 292: 10123-10130

  • DOI: https://doi.org/10.1074/jbc.M117.787754
  • Primary Citation of Related Structures:  
    5N2I

  • PubMed Abstract: 

    F 420 H 2 -dependent enzymes reduce a wide range of substrates that are otherwise recalcitrant to enzyme-catalyzed reduction, and their potential for applications in biocatalysis has attracted increasing attention. Thermobifida fusca is a moderately thermophilic bacterium and holds high biocatalytic potential as a source for several highly thermostable enzymes. We report here on the isolation and characterization of a thermostable F 420 : NADPH oxidoreductase (Tfu-FNO) from T. fusca , the first F 420 -dependent enzyme described from this bacterium. Tfu-FNO was heterologously expressed in Escherichia coli , yielding up to 200 mg of recombinant enzyme per liter of culture. We found that Tfu-FNO is highly thermostable, reaching its highest activity at 65 °C and that Tfu-FNO is likely to act in vivo as an F 420 reductase at the expense of NADPH, similar to its counterpart in Streptomyces griseus We obtained the crystal structure of FNO in complex with NADP + at 1.8 Å resolution, providing the first bacterial FNO structure. The overall architecture and NADP + -binding site of Tfu-FNO were highly similar to those of the Archaeoglobus fulgidus FNO (Af-FNO). The active site is located in a hydrophobic pocket between an N-terminal dinucleotide binding domain and a smaller C-terminal domain. Residues interacting with the 2'-phosphate of NADP + were probed by targeted mutagenesis, indicating that Thr-28, Ser-50, Arg-51, and Arg-55 are important for discriminating between NADP + and NAD + Interestingly, a T28A mutant increased the kinetic efficiency >3-fold as compared with the wild-type enzyme when NADH is the substrate. The biochemical and structural data presented here provide crucial insights into the molecular recognition of the two cofactors, F 420 and NAD(P)H by FNO.


  • Organizational Affiliation

    From the Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Reduced coenzyme F420:NADP oxidoreductase
A, B, C, D
232Thermobifida fusca YXMutation(s): 0 
Gene Names: Tfu_0970
EC: 1.6.99
UniProt
Find proteins for Q47RA9 (Thermobifida fusca (strain YX))
Explore Q47RA9 
Go to UniProtKB:  Q47RA9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ47RA9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B],
L [auth C],
N [auth D]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
K [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth B],
M [auth C],
O [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.167 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.389α = 90
b = 86.089β = 90
c = 136.775γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European CommissionNetherlandsErasmus Mundus Action 2 project for Lot11 - Svaagata.eu
University of GroningenNetherlandsUbbo Emius scholarship

Revision History  (Full details and data files)

  • Version 1.0: 2017-04-26
    Type: Initial release
  • Version 1.1: 2017-06-28
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description