4ZVN

Reduced quinone reductase 2 in complex with acridine orange


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.866 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Binding of DNA-Intercalating Agents to Oxidized and Reduced Quinone Reductase 2.

Leung, K.K.Shilton, B.H.

(2015) Biochemistry 54: 7438-7448

  • DOI: 10.1021/acs.biochem.5b00884
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Quinone reductase 2 (NQO2) is an enzyme that might have intracellular signaling functions. NQO2 can exist in either an oxidized state or a reduced state, and binding of compounds to one or both of these states inhibits enzymatic activity and could al ...

    Quinone reductase 2 (NQO2) is an enzyme that might have intracellular signaling functions. NQO2 can exist in either an oxidized state or a reduced state, and binding of compounds to one or both of these states inhibits enzymatic activity and could also affect intracellular signaling. A wide range of planar aromatic compounds bind NQO2, and we have identified three DNA-intercalating agents [ethidium bromide, acridine orange (AO), and doxorubicin] as novel nanomolar inhibitors of NQO2. Ethidium and AO, which carry a positive charge in their aromatic ring systems, bound reduced NQO2 with an affinity 50-fold higher than that of oxidized NQO2, while doxorubicin bound only oxidized NQO2. Crystallographic analyses of oxidized NQO2 in complex with the inhibitors indicated that the inhibitors were situated deep in the active site. The aromatic faces were sandwiched between the isoalloxazine ring of FAD and the phenyl ring of F178, with their edges making direct contact with residues lining the active site. In reduced NQO2, ethidium and AO occupied a more peripheral position in the active site, allowing several water molecules to interact with the polar end of the negatively charged isoalloxazine ring. We also showed that AO inhibited NQO2 at a nontoxic concentration in cells while ethidium was less effective at inhibiting NQO2 in cells. Together, this study shows that reduced NQO2 has structural and electrostatic properties that yield a preference for binding of planar, aromatic, and positively charged molecules that can also function as DNA-intercalating agents.


    Organizational Affiliation

    Department of Biochemistry, University of Western Ontario , 1151 Richmond Street, London, Ontario, Canada N6A 5C1.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribosyldihydronicotinamide dehydrogenase [quinone]
A, B
230Homo sapiensMutation(s): 0 
Gene Names: NQO2 (NMOR2)
EC: 1.10.5.1
Find proteins for P16083 (Homo sapiens)
Go to Gene View: NQO2
Go to UniProtKB:  P16083
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
FAD
Query on FAD

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

Download SDF File 
Download CCD File 
A, B
ACRIDINE ORANGE
C17 H20 N3
DPKHZNPWBDQZCN-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
AOKd: 0.36 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.866 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.640α = 90.00
b = 82.860β = 90.00
c = 106.230γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
SCALAdata scaling
PHASERphasing
MOSFLMdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-03-30
    Type: Initial release
  • Version 1.1: 2016-06-08
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Database references, Derived calculations, Refinement description