8U19

Crystal structure of SyoA bound to syringol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free: 
    0.182 (Depositor), 0.180 (DCC) 
  • R-Value Work: 
    0.146 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.147 (Depositor) 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Structural insights into S-lignin O-demethylation via a rare class of heme peroxygenase enzymes.

Harlington, A.C.Das, T.Shearwin, K.E.Bell, S.G.Whelan, F.

(2025) Nat Commun 16: 1815-1815

  • DOI: https://doi.org/10.1038/s41467-025-57129-6
  • Primary Citation of Related Structures:  
    8U09, 8U19, 8U1I

  • PubMed Abstract: 

    The O-demethylation of lignin aromatics is a rate-limiting step in their bioconversion to higher-value compounds. A recently discovered cytochrome P450, SyoA, demethylates the S-lignin aromatic syringol. In this work, we solve high-resolution X-ray crystal structures of substrate-free and substrate-bound SyoA and evaluate demethylation of para-substituted S-lignin aromatics via monooxygenase and peroxide shunt pathways. We find that SyoA demethylates S-lignin aromatics exclusively using the peroxide shunt pathway. The atomic-resolution structures reveal the position of non-canonical residues in the I-helix (Gln252, Glu253). Mutagenesis of this amide-acid pair in SyoA shows they are critical for catalytic activity. This work expands the enzymatic toolkit for improving the capacity to funnel lignin derived aromatics towards higher value compounds and defines the chemistry within the active site of the enzyme that enables peroxygenase activity. These insights provide a framework for engineering peroxygenase activity in other heme enzymes to generate easier to use biocatalysts.


  • Organizational Affiliation

    Department of Molecular and Biomedical Science, University of Adelaide, Adelaide, SA, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome P450412Amycolatopsis thermoflava N1165Mutation(s): 0 
EC: 1.14.14.1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
3DM
Query on 3DM

Download Ideal Coordinates CCD File 
C [auth A]2,6-dimethoxyphenol
C8 H10 O3
KLIDCXVFHGNTTM-UHFFFAOYSA-N
NO3
Query on NO3

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
F [auth A],
G [auth A]
NITRATE ION
N O3
NHNBFGGVMKEFGY-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
H [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.26 Å
  • R-Value Free:  0.182 (Depositor), 0.180 (DCC) 
  • R-Value Work:  0.146 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.147 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.851α = 90
b = 62.353β = 103.06
c = 58.71γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentPh2002

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-24
    Type: Initial release
  • Version 1.1: 2025-03-05
    Changes: Database references, Structure summary