7YWU | pdb_00007ywu

Eugenol oxidase from rhodococcus jostii: mutant S81H, A423M, H434Y, S394V, I445D, S518P


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.274 (Depositor), 0.274 (DCC) 
  • R-Value Work: 
    0.227 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7YWU

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Structure- and computational-aided engineering of an oxidase to produce isoeugenol from a lignin-derived compound.

Guo, Y.Alvigini, L.Trajkovic, M.Alonso-Cotchico, L.Monza, E.Savino, S.Maric, I.Mattevi, A.Fraaije, M.W.

(2022) Nat Commun 13: 7195-7195

  • DOI: https://doi.org/10.1038/s41467-022-34912-3
  • Primary Citation Related Structures: 
    7YWU, 7YWV

  • PubMed Abstract: 

    Various 4-alkylphenols can be easily obtained through reductive catalytic fractionation of lignocellulosic biomass. Selective dehydrogenation of 4-n-propylguaiacol results in the formation of isoeugenol, a valuable flavor and fragrance molecule and versatile precursor compound. Here we present the engineering of a bacterial eugenol oxidase to catalyze this reaction. Five mutations, identified from computational predictions, are first introduced to render the enzyme more thermostable. Other mutations are then added and analyzed to enhance chemoselectivity and activity. Structural insight demonstrates that the slow catalytic activity of an otherwise promising enzyme variant is due the formation of a slowly-decaying covalent substrate-flavin cofactor adduct that can be remedied by targeted residue changes. The final engineered variant comprises eight mutations, is thermostable, displays good activity and acts as a highly chemoselective 4-n-propylguaiacol oxidase. We lastly use our engineered biocatalyst in an illustrative preparative reaction at gram-scale. Our findings show that a natural enzyme can be redesigned into a tailored biocatalyst capable of valorizing lignin-based monophenols.


  • Organizational Affiliation
    • Molecular Enzymology Group, University of Groningen, Groningen, the Netherlands.

Macromolecule Content 

  • Total Structure Weight: 479.28 kDa 
  • Atom Count: 33,232 
  • Modeled Residue Count: 4,186 
  • Deposited Residue Count: 4,208 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Probable vanillyl-alcohol oxidase
A, B, C, D, E
A, B, C, D, E, F, G, H
526Rhodococcus jostiiMutation(s): 6 
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ0SBK1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
I7I
(Subject of Investigation/LOI)

Query on I7I



Download:Ideal Coordinates CCD File
O [auth B],
X [auth F]
[[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-5-[5-[(1~{R})-1-(3-methoxy-4-oxidanyl-phenyl)propyl]-7,8-dimethyl-2,4-bis(oxidanylidene)-1~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate
C37 H47 N9 O17 P2
VAUBFXXAVOWJEY-LKEIEZFZSA-N
FAD
(Subject of Investigation/LOI)

Query on FAD



Download:Ideal Coordinates CCD File
AA [auth H]
I [auth A]
P [auth C]
S [auth D]
V [auth E]
AA [auth H],
I [auth A],
P [auth C],
S [auth D],
V [auth E],
Y [auth G]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
EOL
(Subject of Investigation/LOI)

Query on EOL



Download:Ideal Coordinates CCD File
M [auth A],
R [auth C],
U [auth D],
W [auth E],
Z [auth G]
2-methoxy-4-(prop-2-en-1-yl)phenol
C10 H12 O2
RRAFCDWBNXTKKO-UHFFFAOYSA-N
HEZ

Query on HEZ



Download:Ideal Coordinates CCD File
J [auth A],
K [auth A],
N [auth B],
T [auth D]
HEXANE-1,6-DIOL
C6 H14 O2
XXMIOPMDWAUFGU-UHFFFAOYSA-N
GOL

Query on GOL



Download:Ideal Coordinates CCD File
L [auth A],
Q [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.274 (Depositor), 0.274 (DCC) 
  • R-Value Work:  0.227 (Depositor), 0.227 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 149.641α = 90
b = 79.429β = 96.25
c = 189.18γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)European UnionH2020-837890

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-16
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary