9GOZ | pdb_00009goz

4-Allyl syringol oxidase from Streptomyces cavernae: complex with eugenol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.216 (Depositor), 0.216 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 
    0.188 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

Kinetic and structural investigation of the 4-allyl syringol oxidase from Streptomyces cavernae.

Eggerichs, D.Weddeling, H.G.Alvigini, L.Rapsch, T.Weindorf, N.Mattevi, A.Tischler, D.

(2025) Arch Biochem Biophys 765: 110320-110320

  • DOI: https://doi.org/10.1016/j.abb.2025.110320
  • Primary Citation of Related Structures:  
    9GOV, 9GOZ, 9GP0

  • PubMed Abstract: 

    4-Phenol oxidases are proposed to be involved in the utilization of lignin-derived aromatic compounds. While enzymes with selectivity towards 4-hydroxyphenyl and guaiacyl motifs are well described, we identified the first syringyl-specific oxidase from Streptomyces cavernae (Sc4ASO) only very recently. Here, in-depth studies were conducted to unravel the molecular origins of the outstanding selectivity of Sc4ASO. Kinetic experiments revealed high activities on dimethoxylated substrates (up to 2.9 ± 0.1 s -1 ), but also strong cooperativity between both protein subunits, as well as substrate inhibition in dependency of ortho methoxylation and chain length of the para substituent. Rapid mixing kinetics in combination with the determination of the crystal structure in complex with three substrates allowed to connect the kinetic behavior with never-observed positioning of the conserved residue Y471. Ultimately, the catalytic potential of Sc4ASO was investigated in a 100 mL scale cascade reaction to produce the natural product syringaresinol.


  • Organizational Affiliation

    Microbial Biotechnology, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitaetsstrasse 150, 44780, Bochum, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
4-allyl syringol oxidase from Streptomyces cavernae
A, B
554Streptomyces cavernaeMutation(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
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
P6G
Query on P6G

Download Ideal Coordinates CCD File 
E [auth A]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
EOL (Subject of Investigation/LOI)
Query on EOL

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B]
2-methoxy-4-(prop-2-en-1-yl)phenol
C10 H12 O2
RRAFCDWBNXTKKO-UHFFFAOYSA-N
P4G
Query on P4G

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B]
1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
C8 H18 O3
RRQYJINTUHWNHW-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
I [auth B],
J [auth B],
K [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.216 (Depositor), 0.216 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.188 (DCC) 
  • R-Value Observed: 0.188 (Depositor) 
Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.259α = 90
b = 83.259β = 90
c = 297.519γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted EOLClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-05
    Type: Initial release
  • Version 1.1: 2025-02-12
    Changes: Database references