RCSB PDB - 5FXE: Crystal structure of eugenol oxidase in complex with coniferyl alcohol

 5FXE

Crystal structure of eugenol oxidase in complex with coniferyl alcohol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.164 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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This is version 1.2 of the entry. See complete history


Literature

Biocatalytic Properties and Structural Analysis of Eugenol Oxidase from Rhodococcus Jostii Rha1: A Versatile Oxidative Biocatalyst.

Nguyen, Q.De Gonzalo, G.Binda, C.Rioz-Martinez, A.Mattevi, A.Fraaije, M.W.

(2016) Chembiochem 17: 1359

  • DOI: https://doi.org/10.1002/cbic.201600148
  • Primary Citation of Related Structures:  
    5FXD, 5FXE, 5FXF, 5FXP

  • PubMed Abstract: 

    Eugenol oxidase (EUGO) from Rhodococcus jostii RHA1 had previously been shown to convert only a limited set of phenolic compounds. In this study, we have explored the biocatalytic potential of this flavoprotein oxidase, resulting in a broadened substrate scope and a deeper insight into its structural properties. In addition to the oxidation of vanillyl alcohol and the hydroxylation of eugenol, EUGO can efficiently catalyze the dehydrogenation of various phenolic ketones and the selective oxidation of a racemic secondary alcohol-4-(1-hydroxyethyl)-2-methoxyphenol. EUGO was also found to perform the kinetic resolution of a racemic secondary alcohol. Crystal structures of the enzyme in complexes with isoeugenol, coniferyl alcohol, vanillin, and benzoate have been determined. The catalytic center is a remarkable solvent-inaccessible cavity on the si side of the flavin cofactor. Structural comparison with vanillyl alcohol oxidase from Penicillium simplicissimum highlights a few localized changes that correlate with the selectivity of EUGO for phenolic substrates bearing relatively small p-substituents while tolerating o-methoxy substituents.


  • Organizational Affiliation

    Molecular Enzymology, Groningen Biomolecular Sciences and, Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, NL.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EUGENOL OXIDASE
A, B
526Rhodococcus jostii RHA1Mutation(s): 0 
EC: 1.1.3.38
UniProt
Find proteins for Q0SBK1 (Rhodococcus jostii (strain RHA1))
Explore Q0SBK1 
Go to UniProtKB:  Q0SBK1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0SBK1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
CIY
Query on CIY

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]
(2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enal
C10 H10 O3
DKZBBWMURDFHNE-NSCUHMNNSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.161 
  • R-Value Observed: 0.164 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.47α = 90
b = 97.17β = 90
c = 179.05γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing

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 FADClick on this verticalbar to view detailsBest fitted CIYClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.2: 2024-10-09
    Changes: Structure summary