8BAP | pdb_00008bap

Eugenol Oxidase (EUGO) from Rhodococcus jostii RHA1, eightfold mutant active on propanol syringol

PDB DOI: https://doi.org/10.2210/pdb8BAP/pdb

Classification: OXIDOREDUCTASE
Organism(s): Rhodococcus jostii RHA1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2022-10-11 Released: 2023-10-25
Deposition Author(s): Alvigini, L., Mattevi, A.
Funding Organization(s): European Union (EU)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.249 (Depositor), 0.250 (DCC)
R-Value Work:
0.193 (Depositor), 0.193 (DCC)
R-Value Observed:
0.196 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

One-Pot Biocatalytic Synthesis of rac -Syringaresinol from a Lignin-Derived Phenol.

Guo, Y., Alvigini, L., Saifuddin, M., Ashley, B., Trajkovic, M., Alonso-Cotchico, L., Mattevi, A., Fraaije, M.W.

(2023) ACS Catal 13: 14639-14649

PubMed: 38026814 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/acscatal.3c04399
Primary Citation Related Structures:
8BAM, 8BAP

PubMed Abstract:
The drive for a circular bioeconomy has resulted in a great demand for renewable, biobased chemicals. We present a one-pot biocatalytic cascade reaction for the production of racemic syringaresinol, a lignan with applications as a nutraceutical and in polymer chemistry. The process consumes dihydrosinapyl alcohol, which can be produced renewably from the lignocellulosic material. To achieve this, a variant of eugenol oxidase was engineered for the oxidation of dihydrosinapyl alcohol into sinapyl alcohol with good conversion and chemoselectivity. The crystal structure of the engineered oxidase revealed the molecular basis of the influence of the mutations on the chemoselectivity of the oxidation of dihydrosinapyl alcohol. By using horseradish peroxidase, the subsequent oxidative dimerization of sinapyl alcohol into syringaresinol was achieved. Conditions for the one-pot, two-enzyme synthesis were optimized, and a high yield of syringaresinol was achieved by cascading the oxidase and peroxidase steps in a stepwise fashion. This study demonstrates the efficient production of syringaresinol from a compound that can be renewed by reductive catalytic fractionation of lignocellulose, providing a biocatalytic route for generating a valuable compound from lignin.

Organizational Affiliation

Molecular Enzymology Group, University of Groningen, Nijenborgh 4, Groningen, AG 9747, The Netherlands.

Macromolecule Content

Total Structure Weight: 958.81 kDa
Atom Count: 68,547
Modeled Residue Count: 8,400
Deposited Residue Count: 8,416
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable vanillyl-alcohol oxidase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	526	Rhodococcus jostii RHA1	Mutation(s): 8 Gene Names: RHA1_ro03282 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 (Subject of Investigation/LOI) Query on FAD Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain AB [auth N] SDF format, chain DA [auth E] SDF format, chain DB [auth O] SDF format, chain GA [auth F] SDF format, chain GB [auth P] SDF format, chain JA [auth G] SDF format, chain LA [auth H] SDF format, chain NA [auth I] SDF format, chain PA [auth J] SDF format, chain Q [auth A] SDF format, chain SA [auth K] SDF format, chain U [auth B] SDF format, chain UA [auth L] SDF format, chain X [auth C] SDF format, chain XA [auth M] MOL2 format, chain AA [auth D] MOL2 format, chain AB [auth N] MOL2 format, chain DA [auth E] MOL2 format, chain DB [auth O] MOL2 format, chain GA [auth F] MOL2 format, chain GB [auth P] MOL2 format, chain JA [auth G] MOL2 format, chain LA [auth H] MOL2 format, chain NA [auth I] MOL2 format, chain PA [auth J] MOL2 format, chain Q [auth A] MOL2 format, chain SA [auth K] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth L] MOL2 format, chain X [auth C] MOL2 format, chain XA [auth M] mmCIF format, chain AA [auth D] mmCIF format, chain AB [auth N] mmCIF format, chain DA [auth E] mmCIF format, chain DB [auth O] mmCIF format, chain GA [auth F] mmCIF format, chain GB [auth P] mmCIF format, chain JA [auth G] mmCIF format, chain LA [auth H] mmCIF format, chain NA [auth I] mmCIF format, chain PA [auth J] mmCIF format, chain Q [auth A] mmCIF format, chain SA [auth K] mmCIF format, chain U [auth B] mmCIF format, chain UA [auth L] mmCIF format, chain X [auth C] mmCIF format, chain XA [auth M]	AA [auth D] AB [auth N] DA [auth E] DB [auth O] GA [auth F] AA [auth D], AB [auth N], DA [auth E], DB [auth O], GA [auth F], GB [auth P], JA [auth G], LA [auth H], NA [auth I], PA [auth J], Q [auth A], SA [auth K], U [auth B], UA [auth L], X [auth C], XA [auth M]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain AA [auth D] Focus chain AB [auth N] Focus chain DA [auth E] Focus chain DB [auth O] Focus chain GA [auth F] Focus chain GB [auth P] Focus chain JA [auth G] Focus chain LA [auth H] Focus chain NA [auth I] Focus chain PA [auth J] Focus chain Q [auth A] Focus chain SA [auth K] Focus chain U [auth B] Focus chain UA [auth L] Focus chain X [auth C] Focus chain XA [auth M] Interactions & Density Focus chain AA [auth D] Focus chain AB [auth N] Focus chain DA [auth E] Focus chain DB [auth O] Focus chain GA [auth F] Focus chain GB [auth P] Focus chain JA [auth G] Focus chain LA [auth H] Focus chain NA [auth I] Focus chain PA [auth J] Focus chain Q [auth A] Focus chain SA [auth K] Focus chain U [auth B] Focus chain UA [auth L] Focus chain X [auth C] Focus chain XA [auth M]
55B (Subject of Investigation/LOI) Query on 55B Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain BB [auth N] SDF format, chain EA [auth E] SDF format, chain EB [auth O] SDF format, chain HA [auth F] SDF format, chain HB [auth P] SDF format, chain KA [auth G] SDF format, chain MA [auth H] SDF format, chain OA [auth I] SDF format, chain QA [auth J] SDF format, chain R [auth A] SDF format, chain TA [auth K] SDF format, chain V [auth B] SDF format, chain VA [auth L] SDF format, chain Y [auth C] SDF format, chain YA [auth M] MOL2 format, chain BA [auth D] MOL2 format, chain BB [auth N] MOL2 format, chain EA [auth E] MOL2 format, chain EB [auth O] MOL2 format, chain HA [auth F] MOL2 format, chain HB [auth P] MOL2 format, chain KA [auth G] MOL2 format, chain MA [auth H] MOL2 format, chain OA [auth I] MOL2 format, chain QA [auth J] MOL2 format, chain R [auth A] MOL2 format, chain TA [auth K] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth L] MOL2 format, chain Y [auth C] MOL2 format, chain YA [auth M] mmCIF format, chain BA [auth D] mmCIF format, chain BB [auth N] mmCIF format, chain EA [auth E] mmCIF format, chain EB [auth O] mmCIF format, chain HA [auth F] mmCIF format, chain HB [auth P] mmCIF format, chain KA [auth G] mmCIF format, chain MA [auth H] mmCIF format, chain OA [auth I] mmCIF format, chain QA [auth J] mmCIF format, chain R [auth A] mmCIF format, chain TA [auth K] mmCIF format, chain V [auth B] mmCIF format, chain VA [auth L] mmCIF format, chain Y [auth C] mmCIF format, chain YA [auth M]	BA [auth D] BB [auth N] EA [auth E] EB [auth O] HA [auth F] BA [auth D], BB [auth N], EA [auth E], EB [auth O], HA [auth F], HB [auth P], KA [auth G], MA [auth H], OA [auth I], QA [auth J], R [auth A], TA [auth K], V [auth B], VA [auth L], Y [auth C], YA [auth M]	4-[(1E)-3-hydroxyprop-1-en-1-yl]-2,6-dimethoxyphenol C₁₁ H₁₄ O₄ LZFOPEXOUVTGJS-ONEGZZNKSA-N		Interactions Focus chain BA [auth D] Focus chain BB [auth N] Focus chain EA [auth E] Focus chain EB [auth O] Focus chain HA [auth F] Focus chain HB [auth P] Focus chain KA [auth G] Focus chain MA [auth H] Focus chain OA [auth I] Focus chain QA [auth J] Focus chain R [auth A] Focus chain TA [auth K] Focus chain V [auth B] Focus chain VA [auth L] Focus chain Y [auth C] Focus chain YA [auth M] Interactions & Density Focus chain BA [auth D] Focus chain BB [auth N] Focus chain EA [auth E] Focus chain EB [auth O] Focus chain HA [auth F] Focus chain HB [auth P] Focus chain KA [auth G] Focus chain MA [auth H] Focus chain OA [auth I] Focus chain QA [auth J] Focus chain R [auth A] Focus chain TA [auth K] Focus chain V [auth B] Focus chain VA [auth L] Focus chain Y [auth C] Focus chain YA [auth M]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain CA [auth D] SDF format, chain CB [auth N] SDF format, chain FA [auth E] SDF format, chain FB [auth O] SDF format, chain IA [auth F] SDF format, chain RA [auth J] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain W [auth B] SDF format, chain WA [auth L] SDF format, chain Z [auth C] SDF format, chain ZA [auth M] MOL2 format, chain CA [auth D] MOL2 format, chain CB [auth N] MOL2 format, chain FA [auth E] MOL2 format, chain FB [auth O] MOL2 format, chain IA [auth F] MOL2 format, chain RA [auth J] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth L] MOL2 format, chain Z [auth C] MOL2 format, chain ZA [auth M] mmCIF format, chain CA [auth D] mmCIF format, chain CB [auth N] mmCIF format, chain FA [auth E] mmCIF format, chain FB [auth O] mmCIF format, chain IA [auth F] mmCIF format, chain RA [auth J] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain W [auth B] mmCIF format, chain WA [auth L] mmCIF format, chain Z [auth C] mmCIF format, chain ZA [auth M]	CA [auth D] CB [auth N] FA [auth E] FB [auth O] IA [auth F] CA [auth D], CB [auth N], FA [auth E], FB [auth O], IA [auth F], RA [auth J], S [auth A], T [auth A], W [auth B], WA [auth L], Z [auth C], ZA [auth M]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain CB [auth N] Focus chain FA [auth E] Focus chain FB [auth O] Focus chain IA [auth F] Focus chain RA [auth J] Focus chain S [auth A] Focus chain T [auth A] Focus chain W [auth B] Focus chain WA [auth L] Focus chain Z [auth C] Focus chain ZA [auth M] Interactions & Density Focus chain CA [auth D] Focus chain CB [auth N] Focus chain FA [auth E] Focus chain FB [auth O] Focus chain IA [auth F] Focus chain RA [auth J] Focus chain S [auth A] Focus chain T [auth A] Focus chain W [auth B] Focus chain WA [auth L] Focus chain Z [auth C] Focus chain ZA [auth M]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.249 (Depositor), 0.250 (DCC)
R-Value Work: 0.193 (Depositor), 0.193 (DCC)
R-Value Observed: 0.196 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.556	α = 114.87
b = 142.995	β = 97
c = 154.6	γ = 93.28

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-10-25

Deposition Author(s):

Alvigini, L.

Mattevi, A.

Funding Organization	Location	Grant Number
European Union (EU)	European Union	Grant Agreement No. 837890 (SMARTBOX).

Revision History (Full details and data files)

Version 1.0: 2023-10-25
Type: Initial release
Version 1.1: 2023-11-01
Changes: Advisory, Database references, Derived calculations
Version 1.2: 2023-12-13
Changes: Database references
Version 1.3: 2026-03-04
Changes: Refinement description, Structure summary