9FD4 | pdb_00009fd4

flavin reductase ThdF in complex with two bound FADs in space group P212121


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free: 
    0.142 (Depositor), 0.141 (DCC) 
  • R-Value Work: 
    0.121 (Depositor), 0.121 (DCC) 
  • R-Value Observed: 
    0.122 (Depositor) 

Starting Models: experimental
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Ligand Structure Quality Assessment 

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Literature

The NADH-dependent flavin reductase ThdF follows an ordered sequential mechanism though crystal structures reveal two FAD molecules in the active site.

Horstmeier, H.J.Bork, S.Nagel, M.F.Keller, W.Spross, J.Diepold, N.Ruppel, M.Kottke, T.Niemann, H.H.

(2024) J Biological Chem 301: 108128-108128

  • DOI: https://doi.org/10.1016/j.jbc.2024.108128
  • Primary Citation of Related Structures:  
    9FD4, 9FD5, 9FD6

  • PubMed Abstract: 

    Two-component flavin-dependent monooxygenases are of great interest as biocatalysts for the production of pharmaceuticals and other relevant molecules, as they catalyze chemically important reactions such as hydroxylation, epoxidation and halogenation. The monooxygenase components require a separate flavin reductase, which provides the necessary reduced flavin cofactor. The tryptophan halogenase Thal from Streptomyces albogriseolus is a well-characterized two-component flavin-dependent halogenase. Thal exhibits some limitations in terms of halogenation efficiency, also caused by unproductive enzyme-substrate complexes with reduced flavin adenine dinucleotide (FAD). Since the reductase components have an important regulatory function for the activity and efficiency of the monooxygenase by controlling the supply of reduced flavin, here we studied the so far uncharacterized flavin reductase ThdF from the same gene cluster in S. albogriseolus, which potentially cooperates with Thal. A crystal structure of ThdF in complex with both substrates, FAD and NADH, revealed their orientation for hydride transfer. We obtained two further ThdF structures with two FAD molecules bound to the active site, suggesting a ping-pong bi-bi mechanism. In contrast, steady-state enzyme kinetics clearly showed that ThdF catalyzes flavin reduction via an ordered sequential mechanism, with FAD being bound first and FADH 2 released last. Compared to related flavin reductases, ThdF has a low k cat and low K M value. The inhibition of ThdF by NAD + might limit Thal's halogenation activity when the cellular NADH level is low. These results provide first insights into how the efficiency of Thal could be controlled by flavin reduction at the reductase ThdF.


  • Organizational Affiliation

    Structural Biochemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Flavin reductaseA,
B [auth C],
C [auth B],
D
195Streptomyces albogriseolusMutation(s): 0 
Gene Names: thdF
UniProt
Find proteins for A0A1B1V585 (Streptomyces albogriseolus)
Explore A0A1B1V585 
Go to UniProtKB:  A0A1B1V585
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1B1V585
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
J [auth C]
K [auth C]
L [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
N [auth B],
R [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
O [auth B],
S [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.14 Å
  • R-Value Free:  0.142 (Depositor), 0.141 (DCC) 
  • R-Value Work:  0.121 (Depositor), 0.121 (DCC) 
  • R-Value Observed: 0.122 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.79α = 90
b = 83.61β = 90
c = 157.34γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted FADClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyNI 694/10-1

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-25
    Type: Initial release
  • Version 1.1: 2025-01-22
    Changes: Database references
  • Version 1.2: 2025-02-05
    Changes: Database references