5FXF

Crystal structure of eugenol oxidase in complex with benzoate

PDB DOI: https://doi.org/10.2210/pdb5FXF/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.212
R-Value Work: 0.165
R-Value Observed: 0.167

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 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

PubMed: 27123962 Search on PubMedSearch on PubMed Central
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.

Macromolecule Content

Total Structure Weight: 119.75 kDa
Atom Count: 8,689
Modelled Residue Count: 1,050
Deposited Residue Count: 1,052
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q0SBK1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B]	C [auth A], G [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
BEZ Query on BEZ Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B]	D [auth A], H [auth B]	BENZOIC ACID C₇ H₆ O₂ WPYMKLBDIGXBTP-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B]	E [auth A], F [auth A], I [auth B], J [auth B], K [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.212
R-Value Work: 0.165
R-Value Observed: 0.167
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.29	α = 90
b = 96.87	β = 90
c = 179.66	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-07-27

Deposition Author(s):

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