1GQG

Quercetin 2,3-dioxygenase in complex with the inhibitor diethyldithiocarbamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Functional Analysis of the Copper-Dependent Quercetin 2,3-Dioxygenase.1.Ligand-Induced Coordination Changes Probed by X-Ray Crystallography: Inhibition, Ordering Effect and Mechanistic Insights

Steiner, R.A.Kooter, I.M.Dijkstra, B.W.

(2002) Biochemistry 41: 7955

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The crystal structures of the copper-dependent Aspergillus japonicus quercetin 2,3-dioxygenase (2,3QD) complexed with the inhibitors diethyldithiocarbamate (DDC) and kojic acid (KOJ) are reported at 1.70 and 2.15 A resolution, respectively. Both inhi ...

    The crystal structures of the copper-dependent Aspergillus japonicus quercetin 2,3-dioxygenase (2,3QD) complexed with the inhibitors diethyldithiocarbamate (DDC) and kojic acid (KOJ) are reported at 1.70 and 2.15 A resolution, respectively. Both inhibitors asymmetrically chelate the metal center and assume a common orientation in the active site cleft. Their molecular plane blocks access to the inner portion of the cavity which is lined by the side chains of residues Met51, Thr53, Phe75, Phe114, and Met123 and which is believed to bind the flavonol B-ring of the natural substrate. The binding of the inhibitors brings order into the mixed coordination observed in the native enzyme. DDC and KOJ induce a single conformation of the Glu73 side chain, although in different ways. In the presence of DDC, Glu73 is detached from the copper ion with its carboxylate moiety pointing away from the active site cavity. In contrast, when KOJ is bound, Glu73 ligates the Cu ion through its O(epsilon)(1) atom with a monodentate geometry. Compared to the native coordinating conformation, this conformation is approximately 90 degrees rotated about the chi(3) angle. This latter Glu73 conformation is compatible with the presence of a bound substrate.


    Organizational Affiliation

    Laboratory of Biophysical Chemistry, Department of Chemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
QUERCETIN 2,3-DIOXYGENASE
A, B, C, D
350Aspergillus japonicusEC: 1.13.11.24
Find proteins for Q7SIC2 (Aspergillus japonicus)
Go to UniProtKB:  Q7SIC2
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DCD
Query on DCD

Download SDF File 
Download CCD File 
A, B, C, D
DIETHYLCARBAMODITHIOIC ACID
C5 H11 N S2
LMBWSYZSUOEYSN-UHFFFAOYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
A, C
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
CU
Query on CU

Download SDF File 
Download CCD File 
A, B, C, D
COPPER (II) ION
Cu
JPVYNHNXODAKFH-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 108.939α = 90.00
b = 55.646β = 98.26
c = 123.863γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance