5FLI

enzyme-substrate complex of Ni-quercetinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Quercetin 2,4-Dioxygenase Activates Dioxygen in a Side-On O2-Ni Complex.

Jeoung, J.H.Nianios, D.Fetzner, S.Dobbek, H.

(2016) Angew. Chem. Int. Ed. Engl. 55: 3281-3284

  • DOI: 10.1002/anie.201510741
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Quercetin 2,4-dioxygenase (quercetinase) from Streptomyces uses nickel as the active-site cofactor to catalyze oxidative cleavage of the flavonol quercetin. How this unusual active-site metal supports catalysis and O2 activation is under debate. We p ...

    Quercetin 2,4-dioxygenase (quercetinase) from Streptomyces uses nickel as the active-site cofactor to catalyze oxidative cleavage of the flavonol quercetin. How this unusual active-site metal supports catalysis and O2 activation is under debate. We present crystal structures of Ni-quercetinase in three different states, thus providing direct insight into how quercetin and O2 are activated at the Ni(2+) ion. The Ni(2+) ion is coordinated by three histidine residues and a glutamate residue (E(76)) in all three states. Upon binding, quercetin replaces one water ligand at Ni and is stabilized by a short hydrogen bond through E(76) , the carboxylate group of which rotates by 90°. This conformational change weakens the interaction between Ni and the remaining water ligand, thereby preparing a coordination site at Ni to bind O2. O2 binds side-on to the Ni(2+) ion and is perpendicular to the C2-C3 and C3-C4 bonds of quercetin, which are cleaved in the following reaction steps.


    Organizational Affiliation

    Institut für Biologie, Strukturbiologie/Biochemie, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099, Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
QUERCETINASE QUED
A, B, C, D, E, F, G, H, I, J, K, L
186Streptomyces sp. FLAMutation(s): 0 
Gene Names: queD
Find proteins for A2VA43 (Streptomyces sp. FLA)
Go to UniProtKB:  A2VA43
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
QUE
Query on QUE

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, J, K, L
3,5,7,3',4'-PENTAHYDROXYFLAVONE
QUERCETIN
C15 H10 O7
REFJWTPEDVJJIY-UHFFFAOYSA-N
 Ligand Interaction
NI
Query on NI

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.195 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 101.396α = 90.00
b = 113.752β = 96.45
c = 105.003γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2017-04-12
    Type: Database references
  • Version 1.2: 2017-04-26
    Type: Database references
  • Version 1.3: 2017-05-24
    Type: Database references
  • Version 1.4: 2019-02-27
    Type: Data collection, Database references