1D4A

CRYSTAL STRUCTURE OF HUMAN NAD[P]H-QUINONE OXIDOREDUCTASE AT 1.7 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 

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This is version 1.3 of the entry. See complete history


Literature

Structures of recombinant human and mouse NAD(P)H:quinone oxidoreductases: species comparison and structural changes with substrate binding and release.

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

(2000) Proc Natl Acad Sci U S A 97: 3177-3182

  • DOI: 10.1073/pnas.050585797
  • Primary Citation of Related Structures:  
    1D4A, 1DXO, 1DXQ

  • 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 1.7-A resolution) and mouse (2 ...

    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
    • 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
    • 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

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
QUINONE REDUCTASEA, B, C, D273Homo sapiensMutation(s): 0 
Gene Names: NQO1DIA4NMOR1
EC: 1.6.99.2 (PDB Primary Data), 1.6.5.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P15559 (Homo sapiens)
Explore P15559 
Go to UniProtKB:  P15559
PHAROS:  P15559
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.209 
  • R-Value Observed: 0.209 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.678α = 77.04
b = 57.032β = 76.72
c = 97.402γ = 86.89
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
CCP4data 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: 1999-10-15
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2014-11-12
    Changes: Structure summary