2F1O

Crystal Structure of NQO1 with Dicoumarol

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 

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Literature

The crystal structure of NAD(P)H quinone oxidoreductase 1 in complex with its potent inhibitor dicoumarol.

Asher, G., Dym, O., Tsvetkov, P., Adler, J., Shaul, Y.

(2006) Biochemistry 45: 6372-6378

  • DOI: 10.1021/bi0600087
  • Primary Citation of Related Structures:  
    2F1O

  • PubMed Abstract: 

    • NAD(P)H quinone oxidoreductase 1 (NQO1) is a ubiquitous flavoenzyme that catalyzes two-electron reduction of quinones to hydroquinones utilizing NAD(P)H as an electron donor. NQO1 binds and stabilizes several short-lived proteins including the tumor suppressors p53 and p73 and the enzyme ornithine decarboxylase (ODC) ...

    NAD(P)H quinone oxidoreductase 1 (NQO1) is a ubiquitous flavoenzyme that catalyzes two-electron reduction of quinones to hydroquinones utilizing NAD(P)H as an electron donor. NQO1 binds and stabilizes several short-lived proteins including the tumor suppressors p53 and p73 and the enzyme ornithine decarboxylase (ODC). Dicoumarol is a widely used potent competitive inhibitor of NQO1 enzymatic activity, which competes with NAD(P)H for binding to NQO1. Dicoumarol also disrupts the binding of NQO1 to p53, p73, and ODC and induces their ubiquitin-independent proteasomal degradation. We report here the crystal structure of human NQO1 in complex with dicoumarol at 2.75 A resolution. We have identified the interactions of dicoumarol with the different residues of NQO1 and the conformational changes imposed upon dicoumarol binding. The most prominent conformational changes that occur in the presence of dicoumarol involve Tyr 128 and Phe 232 that are present on the surface of the NQO1 catalytic pocket. On the basis of the comparison of the NQO1 structure in complex with different NQO1 inhibitors and our previous analysis of NQO1 mutants, we propose that the specific conformation of Tyr 128 and Phe 232 is important for NQO1 interaction with p53 and other client proteins.

    Organizational Affiliation: 

    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD(P)H dehydrogenase [quinone] 1
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
273Homo sapiensMutation(s): 0 
Gene Names: NQO1, DIA4, NMOR1
EC: 1.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P15559 (Homo sapiens)
Explore P15559 
Go to UniProtKB:  P15559
PHAROS:  P15559
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15559
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD
Download Ideal Coordinates CCD File 
J [auth A],
L [auth B],
N [auth C],
P [auth D],
S [auth E],
J [auth A],
L [auth B],
N [auth C],
P [auth D],
S [auth E],
T [auth F],
V [auth G],
X [auth H]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N		 Ligand Interaction
DTC
Query on DTC
Download Ideal Coordinates CCD File 
I [auth A],
K [auth B],
M [auth C],
O [auth D],
Q [auth E],
I [auth A],
K [auth B],
M [auth C],
O [auth D],
Q [auth E],
R [auth E],
U [auth G],
W [auth H]
BISHYDROXY[2H-1-BENZOPYRAN-2-ONE,1,2-BENZOPYRONE]
C19 H12 O6
HIZKPJUTKKJDGA-BETUJISGSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.244α = 91.14
b = 86.187β = 107.91
c = 100.562γ = 93.17
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-16
    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: 2011-10-19
    Changes: Structure summary