WrbA from Escherichia coli, Benzoquinone complex

Experimental Data Snapshot

  • Resolution: 1.99 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

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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: https://doi.org/10.1128/JB.01336-07
  • Primary Citation of Related Structures:  
    3B6I, 3B6J, 3B6K, 3B6M

  • 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 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

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Flavoprotein wrbA
A, B
198Escherichia coli K-12Mutation(s): 0 
Find proteins for P0A8G6 (Escherichia coli (strain K12))
Explore P0A8G6 
Go to UniProtKB:  P0A8G6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A8G6
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 15P

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
I [auth B],
J [auth B]
C69 H140 O35
Query on FMN

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
C17 H21 N4 O9 P
Query on PLQ

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
C6 H4 O2
Experimental Data & Validation

Experimental Data

  • Resolution: 1.99 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.239α = 90
b = 94.239β = 90
c = 175.554γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-12-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Source and taxonomy, Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description