3B6K

WrbA from Escherichia coli, Benzoquinone complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the NADH:quinone oxidoreductase WrbA from Escherichia coli.

Andrade, S.L.Patridge, E.V.Ferry, J.G.Einsle, O.

(2007) J.Bacteriol. 189: 9101-9107

  • DOI: 10.1128/JB.01336-07
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The flavoprotein WrbA, originally described as a tryptophan (W) repressor-binding protein in Escherichia coli, has recently been shown to exhibit the enzymatic activity of a NADH:quinone oxidoreductase. This finding points toward a possible role in s ...

    The flavoprotein WrbA, originally described as a tryptophan (W) repressor-binding protein in Escherichia coli, has recently been shown to exhibit the enzymatic activity of a NADH:quinone oxidoreductase. This finding points toward a possible role in stress response and in the maintenance of a supply of reduced quinone. We have determined the three-dimensional structure of the WrbA holoprotein from E. coli at high resolution (1.66 A), and we observed a characteristic, tetrameric quaternary structure highly similar to the one found in the WrbA homologs of Deinococcus radiodurans and Pseudomonas aeruginosa. A similar tetramer was originally observed in an iron-sulfur flavoprotein involved in the reduction of reactive oxygen species. Together with other, recently characterized proteins such as YhdA or YLR011wp (Lot6p), these tetrameric flavoproteins may constitute a large family with diverse functions in redox catalysis. WrbA binds substrates at an active site that provides an ideal stacking environment for aromatic moieties, while providing a pocket that is structured to stabilize the ADP part of an NADH molecule in its immediate vicinity. Structures of WrbA in complex with benzoquinone and NADH suggest a sequential binding mechanism for both molecules in the catalytic cycle.


    Organizational Affiliation

    Institute for Microbiology and Genetics, Georg August University Göttingen, Justus von Liebig Weg 11, 37077 Göttingen, Germany. susana.andrade@bio.uni-goettingen.de




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Flavoprotein wrbA
A, B
198Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: wrbA
EC: 1.6.5.2
Find proteins for P0A8G6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8G6
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLQ
Query on PLQ

Download SDF File 
Download CCD File 
A, B
1,4-benzoquinone
cyclohexa-2,5-diene-1,4-dione; QUINONE RING OF THE PLASTOQUINONE 9
C6 H4 O2
AZQWKYJCGOJGHM-UHFFFAOYSA-N
 Ligand Interaction
FMN
Query on FMN

Download SDF File 
Download CCD File 
A, B
FLAVIN MONONUCLEOTIDE
RIBOFLAVIN MONOPHOSPHATE
C17 H21 N4 O9 P
FVTCRASFADXXNN-SCRDCRAPSA-N
 Ligand Interaction
15P
Query on 15P

Download SDF File 
Download CCD File 
A, B
POLYETHYLENE GLYCOL (N=34)
PEG 1500
C69 H140 O35
VUYXVWGKCKTUMF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.99 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.172 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 94.239α = 90.00
b = 94.239β = 90.00
c = 175.554γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-12-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance