1DXO

Crystal structure of human NAD[P]H-QUINONE oxidoreductase CO with 2,3,5,6,tetramethyl-P-benzoquinone (duroquinone) at 2.5 Angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of Recombinant Mouse and Human Nad(P)H:Quinone Oxidoreductases:Species Comparison and Structural Changes with Substrate Binding and Release

Faig, M.Bianchet, M.A.Chen, S.Winski, S.Ross, D.Talalay, P.Amzel, L.M.

(2000) Proc Natl Acad Sci U S A 97: 3177

  • DOI: 10.1073/pnas.050585797
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • NAD(P)H/quinone acceptor oxidoreductase (QR1, NQO1, formerly DT-diaphorase; EC ) protects animal cells from the deleterious and carcinogenic effects of quinones and other electrophiles. In this paper we report the apoenzyme structures of human (at 1. ...

    NAD(P)H/quinone acceptor oxidoreductase (QR1, NQO1, formerly DT-diaphorase; EC ) protects animal cells from the deleterious and carcinogenic effects of quinones and other electrophiles. In this paper we report the apoenzyme structures of human (at 1.7-A resolution) and mouse (2.8 A) QR1 and the complex of the human enzyme with the substrate duroquinone (2.5 A) (2,3,5, 6-tetramethyl-p-benzoquinone). In addition to providing a description and rationale of the structural and catalytic differences among several species, these structures reveal the changes that accompany substrate or cofactor (NAD) binding and release. Tyrosine-128 and the loop spanning residues 232-236 close the binding site, partially occupying the space left vacant by the departing molecule (substrate or cofactor). These changes highlight the exquisite control of access to the catalytic site that is required by the ping-pong mechanism in which, after reducing the flavin, NAD(P)(+) leaves the catalytic site and allows substrate to bind at the vacated position. In the human QR1-duroquinone structure one ring carbon is significantly closer to the flavin N5, suggesting a direct hydride transfer to this atom.


    Related Citations: 
    • Structure and Mechanism of Cytosolic Quinone Reductase
      Bianchet, M.A., Foster, C., Faig, M., Talalay, P., Amzel, L.M.
      (1999) Biochem Soc Trans 27: 610
    • Crystal Structure of Human Quinone Reductase Type 2, a Metalloprotein
      Foster, C., Bianchet, M.A., Talalay, P., Zhao, Q., Amzel, L.M.
      (1999) Biochemistry 38: 9881
    • The Three-Dimensional Structure of Nad(P)H:Quinone Reductase, a Flavoprotein Involved in Cancer Chemoprotection and Chemotherapy: Mechanism of Two-Electron Reduction
      Li, R., Bianchet, M.A., Talalay, P., Amzel, L.M.
      (1995) Proc Natl Acad Sci U S A 92: 8846

    Organizational Affiliation

    Departments of Biophysics and Biophysical Chemistry and Pharmacology and Molecular Sciences, Johns Hopkins Medical School, Baltimore, MD 21205, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
QUINONE REDUCTASE
A, B, C, D
273Homo sapiensMutation(s): 0 
Gene Names: NQO1DIA4NMOR1
EC: 1.6.99.2 (PDB Primary Data), 1.6.5.2 (UniProt)
Find proteins for P15559 (Homo sapiens)
Go to UniProtKB:  P15559
NIH Common Fund Data Resources
PHAROS  P15559
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download CCD File 
A, B, C, D
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
 Ligand Interaction
DQN
Query on DQN

Download CCD File 
A, B, C, D
DUROQUINONE
C10 H12 O2
WAMKWBHYPYBEJY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.579α = 76.24
b = 56.912β = 76.73
c = 97.755γ = 86.33
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-04-23
    Type: Initial release
  • Version 1.1: 2014-11-12
    Changes: Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance
  • Version 1.2: 2017-07-05
    Changes: Data collection