2B3D

Crystal structure of Modulator of Drug activity B in complex with flavin adenine dinucleotide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

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This is version 1.5 of the entry. See complete history


Literature

Modulator of drug activity B from Escherichia coli: crystal structure of a prokaryotic homologue of DT-diaphorase.

Adams, M.A.Jia, Z.

(2006) J Mol Biol 359: 455-465

  • DOI: https://doi.org/10.1016/j.jmb.2006.03.053
  • Primary Citation of Related Structures:  
    2AMJ, 2B3D

  • PubMed Abstract: 

    Modulator of drug activity B (MdaB) is a putative member of the DT-diaphorase family of NAD(P)H:oxidoreductases that afford cellular protection against quinonoid compounds. While there have been extensive investigations of mammalian homologues, putative prokaryotic members of this enzyme family have received little attention. The three-dimensional crystal structure of apo-MdaB reported herein exhibits significant structural similarity to a number of flavoproteins, including the mammalian DT-diaphorases. We have shown by mass spectrometry that the endogenously associated cofactor is flavin adenine dinucleotide and we present here the structure of MdaB in complex with this compound. Growth of Escherichia coli carrying null mutations in the genes encoding MdaB or quinol monooxygenase, the gene for which shares the mdaB promoter, were not affected by the presence of menadione. However, over-expression of recombinant quinol monooxygenase conferred a state of resistance against both tetracycline and adriamycin. This work suggests that the redox cycle formed by these proteins protects E. coli from the toxic effects of polyketide compounds rather than the oxidative stress of menadione alone.


  • Organizational Affiliation

    Department of Biochemistry, Queen's University, Kingston, Ont., Canada K7L 3N6.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Modulator of drug activity B
A, B
204Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0AEY5 (Escherichia coli (strain K12))
Explore P0AEY5 
Go to UniProtKB:  P0AEY5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AEY5
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.261 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.626α = 90
b = 84.105β = 110.95
c = 55.49γ = 90
Software Package:
Software NamePurpose
MAR345data collection
SCALEPACKdata scaling
PHASERphasing
CNSrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-08-29
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2023-05-31
    Changes: Database references, Derived calculations
  • Version 1.5: 2023-09-20
    Changes: Data collection, Refinement description