9G89 | pdb_00009g89

Carotenoid cleavage oxygenase from Moesziomyces aphidis bound to vanillin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free: 
    0.194 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.163 (Depositor), 0.163 (DCC) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural and Functional Characteristics of Potent Dioxygenase from Moesziomyces aphidis .

Schober, L.Plewka, J.Sriwaiyaphram, K.Bielec, B.Schiefer, A.Wongnate, T.Magiera-Mularz, K.Rudroff, F.Winkler, M.

(2025) JACS Au 5: 3014-3020

  • DOI: https://doi.org/10.1021/jacsau.5c00456
  • Primary Citation of Related Structures:  
    9G88, 9G89, 9G8A, 9G8F

  • PubMed Abstract: 

    Enzymatic C=C double bond cleavage to give carbonyl-species is an emerging alternative to ozonolysis, or stoichiometric use of metal-oxidants. The substrate scope of 4-His Fe dioxygenases, however, appears to be restricted to aromatic compounds with a hydroxy group at the 4-position of the aromatic ring. In-depth structural and functional characterization is a prerequisite to understand and ultimately to extend the substrate scope of this family of enzymes. Herein, Moesziomyces aphidis DSM 70725 aromatic dioxygenase ( Map ADO) is characterized through X-ray crystallography, biophysical as well as biochemical assays, substrate docking and mutagenesis. Map ADO features a seven-bladed β-propeller fold and a Fe 2+ center coordinated by four histidine residues and shares a conserved structural motif with homologous enzymes despite low sequence identity (<38%). Fe 2+ is tightly bound and present in the catalytically active oxidation state at ambient conditions. Map ADO is robust and retains activity for several freeze/thaw cycles. Map ADO's interaction with ligands 4-hydroxybenzaldehyde, ortho -vanillin and vanillin indicate that hydrogen-bonding of the phenolic OH group is key to activity. Structural analysis and site-directed mutagenesis indicate that two key residues (Y136 and K169), and the substrate's hydroxy group, are essential for accurately positioning the double bond toward the activated oxygen at the Fe center. Map ADO wild-type exhibits the highest reported activity for converting isoeugenol to vanillin (231 μmol min -1 mg -1 ).


  • Organizational Affiliation

    Institute of Molecular Biotechnology, Graz University of Technology, NAWI Graz, Petersgasse 14, 8010 Graz, Austria.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lignostilbene dioxygenase
A, B
556Moesziomyces aphidisMutation(s): 0 
Gene Names: PaG_05861
UniProt
Find proteins for W3VHW6 (Moesziomyces aphidis)
Explore W3VHW6 
Go to UniProtKB:  W3VHW6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW3VHW6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
V55 (Subject of Investigation/LOI)
Query on V55

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
4-hydroxy-3-methoxybenzaldehyde
C8 H8 O3
MWOOGOJBHIARFG-UHFFFAOYSA-N
GOL (Subject of Investigation/LOI)
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
FE2 (Subject of Investigation/LOI)
Query on FE2

Download Ideal Coordinates CCD File 
I [auth A],
L [auth B]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.67 Å
  • R-Value Free:  0.194 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.163 (Depositor), 0.163 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.68α = 90
b = 84.676β = 108.349
c = 106.571γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Austrian Science FundAustriaP33687

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release
  • Version 1.1: 2025-08-13
    Changes: Database references