3U7R

FerB - flavoenzyme NAD(P)H:(acceptor) oxidoreductase (FerB) from Paracoccus denitrificans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Structural and Functional Basis of Catalysis Mediated by NAD(P)H:acceptor Oxidoreductase (FerB) of Paracoccus denitrificans.

Sedlacek, V.Klumpler, T.Marek, J.Kucera, I.

(2014) Plos One 9: e96262-e96262

  • DOI: 10.1371/journal.pone.0096262

  • PubMed Abstract: 
  • FerB from Paracoccus denitrificans is a soluble cytoplasmic flavoprotein that accepts redox equivalents from NADH or NADPH and transfers them to various acceptors such as quinones, ferric complexes and chromate. The crystal structure and small-angle ...

    FerB from Paracoccus denitrificans is a soluble cytoplasmic flavoprotein that accepts redox equivalents from NADH or NADPH and transfers them to various acceptors such as quinones, ferric complexes and chromate. The crystal structure and small-angle X-ray scattering measurements in solution reported here reveal a head-to-tail dimer with two flavin mononucleotide groups bound at the opposite sides of the subunit interface. The dimers tend to self-associate to a tetrameric form at higher protein concentrations. Amino acid residues important for the binding of FMN and NADH and for the catalytic activity are identified and verified by site-directed mutagenesis. In particular, we show that Glu77 anchors a conserved water molecule in close proximity to the O2 of FMN, with the probable role of facilitating flavin reduction. Hydride transfer is shown to occur from the 4-pro-S position of NADH to the solvent-accessible si side of the flavin ring. When using deuterated NADH, this process exhibits a kinetic isotope effect of about 6 just as does the NADH-dependent quinone reductase activity of FerB; the first, reductive half-reaction of flavin cofactor is thus rate-limiting. Replacing the bulky Arg95 in the vicinity of the active site with alanine substantially enhances the activity towards external flavins that obeys the standard bi-bi ping-pong reaction mechanism. The new evidence for a cryptic flavin reductase activity of FerB justifies the previous inclusion of this enzyme in the protein family of NADPH-dependent FMN reductases.


    Organizational Affiliation

    Department of Biochemistry, Faculty of Science, Masaryk University, Brno, Czech Republic.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADPH-dependent FMN reductase
A, B
190Paracoccus denitrificans (strain Pd 1222)Mutation(s): 0 
Find proteins for A1B9E3 (Paracoccus denitrificans (strain Pd 1222))
Go to UniProtKB:  A1B9E3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2PE
Query on 2PE

Download SDF File 
Download CCD File 
A
NONAETHYLENE GLYCOL
C18 H38 O10
YZUUTMGDONTGTN-UHFFFAOYSA-N
 Ligand Interaction
FNR
Query on FNR

Download SDF File 
Download CCD File 
A, B
1-DEOXY-1-(7,8-DIMETHYL-2,4-DIOXO-3,4-DIHYDRO-2H-BENZO[G]PTERIDIN-1-ID-10(5H)-YL)-5-O-PHOSPHONATO-D-RIBITOL
TWO ELECTRON REDUCED FLAVIN MONONUCLEOTIDE
C17 H23 N4 O9 P
YTNIXZGTHTVJBW-SCRDCRAPSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.174 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 61.030α = 90.00
b = 89.140β = 90.00
c = 71.280γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Auto-Rickshawphasing
XDSdata scaling
MAR345data collection
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-10-24
    Type: Initial release
  • Version 1.1: 2014-05-21
    Type: Database references, Derived calculations
  • Version 1.2: 2017-11-08
    Type: Refinement description