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 
  • R-Value Observed: 0.197 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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
A, B, C, D, E, F, G, H, I, J, K, L
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]
BA [auth H],
EA [auth J],
GA [auth K],
IA [auth L],
N [auth A],
P [auth B],
R [auth C],
T [auth D],
V [auth E],
X [auth F],
Z [auth G]
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]
AA [auth H],
CA [auth I],
DA [auth J],
FA [auth K],
HA [auth L],
M [auth A],
O [auth B],
Q [auth C],
S [auth D],
U [auth E],
W [auth F],
Y [auth G]
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 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • 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

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Ligand Structure Quality Assessment 


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