1D4A

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

• PDB DOI:  https://doi.org/10.2210/pdb1D4A/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1999-10-01 Released: 1999-10-15 
• Deposition Author(s): Faig, M., Bianchet, M.A., Chen, S., Winski, S., Ross, D., Amzel, L.M.

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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 

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

• PubMed: 10706635 
• DOI: https://doi.org/10.1073/pnas.97.7.3177
• 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 (2.8 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.

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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

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 126.25 kDa 
• Atom Count: 9,496 
• Modelled Residue Count: 1,092 
• Deposited Residue Count: 1,092 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
QUINONE REDUCTASE	A, B, C, D	273	Homo sapiens	Mutation(s): 0  Gene Names: NQO1, DIA4, NMOR1 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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	E [auth A], F [auth B], G [auth C], H [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N

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 = 55.678	α = 77.04
b = 57.032	β = 76.72
c = 97.402	γ = 86.89

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
DENZO	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-10-15 
Deposition Author(s): Faig, M., Bianchet, M.A., Chen, S., Winski, S., Ross, D., Amzel, L.M.

Revision History  

• 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