9FFE | pdb_00009ffe

Carbohydrate active oxidoreductases from Phytophthora sojae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 
    0.226 (Depositor), 0.228 (DCC) 
  • R-Value Work: 
    0.174 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.176 (Depositor) 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Enzymatic oxidation of galacturonides from pectin breakdown contributes to stealth infection by Oomycota phytopathogens.

Turella, S.He, C.Zhao, L.Banerjee, S.Plouhinec, L.Assiah Yao, R.Norgaard Kejlstrup, M.C.Grisel, S.So, Y.Annic, B.Fanuel, M.Haddad Momeni, M.Bissaro, B.Meier, S.Morth, J.P.Dong, S.Berrin, J.G.Abou Hachem, M.

(2025) Nat Commun 16: 3467-3467

  • DOI: https://doi.org/10.1038/s41467-025-58668-8
  • Primary Citation of Related Structures:  
    8S6G, 8S6S, 8S71, 9FFE

  • PubMed Abstract: 

    Phytophthora phytopathogens from Oomycota cause devastating crop losses and threaten food security. However, Phytophthora secreted proteins that interact with plant-hosts remain underexplored. Here, auxiliary activity family 7 (AA7) enzymes from Ascomycota and Oomycota phytopathogens were shown to oxidise pectin-derived galacturonic acid and/or oligogalacturonides (OGs). Unique mono-cysteinyl-FAD oxidases with positively-charged active sites, suited to oxidise OGs, were discovered in Phytophthora sojae. The P. sojae OG oxidase genes, prevalent in this genus, were co-transcribed with pectin-degradation counterparts during early infection of soybean. Single OG oxidase knockouts significantly decreased P. sojae biomass in planta, potentially linking OG oxidases to virulence. We propose that oxidation by AA7 enzymes impairs the elicitor activity of OGs, potentially contributing to stealth Oomycota infection. Oxidation of OGs unravels a previously unknown microbial mechanism that contributes to evade plant immune-response against pathogens. Our findings highlight a unique oxidase architecture and hitherto unexplored targets for bioprotection from major plant pathogens.


  • Organizational Affiliation

    Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FAD-binding PCMH-type domain-containing protein479Phytophthora sojaeMutation(s): 0 
Gene Names: PHYSODRAFT_474098PHYSODRAFT_476693
UniProt
Find proteins for G4YQ65 (Phytophthora sojae (strain P6497))
Explore G4YQ65 
Go to UniProtKB:  G4YQ65
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG4YQ65
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD (Subject of Investigation/LOI)
Query on FAD

Download Ideal Coordinates CCD File 
C [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A],
E [auth A],
F [auth A],
G [auth A]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
MAN (Subject of Investigation/LOI)
Query on MAN

Download Ideal Coordinates CCD File 
H [auth A]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
OXY (Subject of Investigation/LOI)
Query on OXY

Download Ideal Coordinates CCD File 
D [auth A]OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free:  0.226 (Depositor), 0.228 (DCC) 
  • R-Value Work:  0.174 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.176 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.045α = 88.1
b = 50.5β = 68.13
c = 53.092γ = 74.28
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Novo Nordisk FoundationDenmarkNNF20OC0064747

Revision History  (Full details and data files)

  • Version 1.0: 2025-03-12
    Type: Initial release
  • Version 1.1: 2025-05-14
    Changes: Database references