4LTD

Crystal structures of NADH:FMN oxidoreductase (EMOB) - apo form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.186 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


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Literature

Crystal structures of NADH:FMN oxidoreductase (EmoB) at different stages of catalysis.

Nissen, M.S.Youn, B.Knowles, B.D.Ballinger, J.W.Jun, S.Y.Belchik, S.M.Xun, L.Kang, C.

(2008) J.Biol.Chem. 283: 28710-28720

  • DOI: 10.1074/jbc.M804535200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • EDTA has become a major organic pollutant in the environment because of its extreme usage and resistance to biodegradation. Recently, two critical enzymes, EDTA monooxygenase (EmoA) and NADH:FMN oxidoreductase (EmoB), belonging to the newly establish ...

    EDTA has become a major organic pollutant in the environment because of its extreme usage and resistance to biodegradation. Recently, two critical enzymes, EDTA monooxygenase (EmoA) and NADH:FMN oxidoreductase (EmoB), belonging to the newly established two-component flavin-diffusible monooxygenase family, were identified in the EDTA degradation pathway in Mesorhizobium sp. BNC1. EmoA is an FMNH2-dependent enzyme that requires EmoB to provide FMNH2 for the conversion of EDTA to ethylenediaminediacetate. To understand the molecular basis of this FMN-mediated reaction, the crystal structures of the apo-form, FMN.FMN complex, and FMN.NADH complex of EmoB were determined at 2.5 angstroms resolution. The structure of EmoB is a homotetramer consisting of four alpha/beta-single-domain monomers of five parallel beta-strands flanked by five alpha-helices, which is quite different from those of other known two-component flavin-diffusible monooxygenase family members, such as PheA2 and HpaC, in terms of both tertiary and quaternary structures. For the first time, the crystal structures of both the FMN.FMN and FMN.NADH complexes of an NADH:FMN oxidoreductase were determined. Two stacked isoalloxazine rings and nicotinamide/isoalloxazine rings were at a proper distance for hydride transfer. The structures indicated a ping-pong reaction mechanism, which was confirmed by activity assays. Thus, the structural data offer detailed mechanistic information for hydride transfer between NADH to an enzyme-bound FMN and between the bound FMNH2 and a diffusible FMN.


    Organizational Affiliation

    School of Molecular Biosciences, Washington State University, Pullman, Washington 99164-4660, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NADH-dependent FMN reductase
A
197EDTA-degrading bacterium BNC1Mutation(s): 0 
Gene Names: emoB
Find proteins for Q9F9T2 (EDTA-degrading bacterium BNC1)
Go to UniProtKB:  Q9F9T2
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.186 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.169 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 100.925α = 90.00
b = 100.925β = 90.00
c = 129.610γ = 120.00
Software Package:
Software NamePurpose
CrystalCleardata scaling
PHENIXrefinement
X-PLORmodel building
CrystalCleardata reduction
ADSCdata collection
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-08-07
    Type: Initial release