5FXE | pdb_00005fxe

Crystal structure of eugenol oxidase in complex with coniferyl alcohol

• PDB DOI: https://doi.org/10.2210/pdb5FXE/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rhodococcus jostii RHA1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-03-01 Released: 2016-07-27 
• Deposition Author(s): Nguyen, Q.-T., de Gonzalo, G., Binda, C., Martinez, A.R., Mattevi, A., Fraaije, M.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.211 (Depositor), 0.221 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.172 (DCC) 
• R-Value Observed: 
  0.164 (Depositor) 

Starting Model: experimental

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

• PubMed: 27123962 
• DOI: https://doi.org/10.1002/cbic.201600148
• Primary Citation 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.

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Organizational Affiliation: 
• Molecular Enzymology, Groningen Biomolecular Sciences and, Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, NL.
Department of Biology and Biotechnology, University of Pavia, Via Ferrata 1, 27100, Pavia, Italy.
Departmento de Química Orgánica, Universidad de Sevilla, c/Profesor García González 1, 41012, Sevilla, Spain.
Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, NL.
Department of Biology and Biotechnology, University of Pavia, Via Ferrata 1, 27100, Pavia, Italy. [e-mail].
Molecular Enzymology, Groningen Biomolecular Sciences and, Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, NL. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 119.96 kDa 
• Atom Count: 8,891 
• Modeled Residue Count: 1,050 
• Deposited Residue Count: 1,052 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EUGENOL OXIDASE	A, B	526	Rhodococcus jostii RHA1	Mutation(s): 0  EC: 1.1.3.38
UniProt
Find proteins for Q0SBK1 (Rhodococcus jostii (strain RHA1)) Explore Q0SBK1  Go to UniProtKB:  Q0SBK1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	C [auth A], I [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
CIY	D [auth A], J [auth B]	(2E)-3-(4-hydroxy-3-methoxyphenyl)prop-2-enal C10 H10 O3 DKZBBWMURDFHNE-NSCUHMNNSA-N
GOL	E [auth A], F [auth A], G [auth A], H [auth A], K [auth B], L [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 (Depositor), 0.221 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.172 (DCC) 
• R-Value Observed: 0.164 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.47	α = 90
b = 97.17	β = 90
c = 179.05	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-07-27 
Deposition Author(s): Nguyen, Q.-T., de Gonzalo, G., Binda, C., Martinez, A.R., Mattevi, A., Fraaije, M.W.

Revision History  

• 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