5FLI

enzyme-substrate complex of Ni-quercetinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 
    0.232 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted QUEClick on this verticalbar to view details

This is version 1.5 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: https://doi.org/10.1002/anie.201510741
  • Primary Citation of Related Structures:  
    5FLH, 5FLI, 5FLJ

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
QUERCETINASE QUED
A, B, C, D, E
186Streptomyces sp. FLAMutation(s): 0 
EC: 1.13.11.24
UniProt
Find proteins for A2VA43 (Streptomyces sp. FLA)
Explore A2VA43 
Go to UniProtKB:  A2VA43
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2VA43
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QUE
Query on QUE

Download Ideal Coordinates CCD File 
BA [auth H]
EA [auth J]
GA [auth K]
IA [auth L]
N [auth A]
3,5,7,3',4'-PENTAHYDROXYFLAVONE
C15 H10 O7
REFJWTPEDVJJIY-UHFFFAOYSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
AA [auth H]
CA [auth I]
DA [auth J]
FA [auth K]
HA [auth L]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free:  0.232 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.396α = 90
b = 113.752β = 96.45
c = 105.003γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted QUEClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-01
    Type: Initial release
  • Version 1.1: 2017-04-12
    Changes: Database references
  • Version 1.2: 2017-04-26
    Changes: Database references
  • Version 1.3: 2017-05-24
    Changes: Database references
  • Version 1.4: 2019-02-27
    Changes: Data collection, Database references
  • Version 1.5: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description