5FLJ

enzyme-substrate-dioxygen complex of Ni-quercetinase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

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

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

(2016) Angew Chem Int Ed Engl 55: 3281

  • 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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
QUE
Query on QUE

Download Ideal Coordinates CCD File 
BA [auth E]
FA [auth F]
JA [auth G]
MA [auth H]
N [auth A]
BA [auth E],
FA [auth F],
JA [auth G],
MA [auth H],
N [auth A],
Q [auth B],
QA [auth I],
T [auth C],
TA [auth J],
W [auth D],
WA [auth K],
ZA [auth L]
3,5,7,3',4'-PENTAHYDROXYFLAVONE
C15 H10 O7
REFJWTPEDVJJIY-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
AB [auth L]
CA [auth E]
DA [auth E]
HA [auth F]
KA [auth G]
AB [auth L],
CA [auth E],
DA [auth E],
HA [auth F],
KA [auth G],
NA [auth H],
O [auth A],
OA [auth H],
R [auth B],
RA [auth I],
UA [auth J],
X [auth D],
XA [auth K],
Y [auth D],
Z [auth D]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
NI
Query on NI

Download Ideal Coordinates CCD File 
AA [auth E]
EA [auth F]
IA [auth G]
LA [auth H]
M [auth A]
AA [auth E],
EA [auth F],
IA [auth G],
LA [auth H],
M [auth A],
P [auth B],
PA [auth I],
S [auth C],
SA [auth J],
V [auth D],
VA [auth K],
YA [auth L]
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
OXY
Query on OXY

Download Ideal Coordinates CCD File 
GA [auth F],
U [auth C]
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.812α = 90
b = 114.586β = 95.61
c = 105.99γ = 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: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description