8S6S | pdb_00008s6s

Oxidoreductase from Phytophthora sojae

• PDB DOI: https://doi.org/10.2210/pdb8S6S/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Phytophthora sojae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-02-28 Released: 2025-03-12 
• Deposition Author(s): Banerjee, S., Turella, S., Morth, J.P., Abou Hachem, M.
• Funding Organization(s): Novo Nordisk Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free: 
  0.202 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.161 (Depositor), 0.172 (DCC) 

Starting Model: experimental

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

• PubMed: 40216756 
• 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.

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Organizational Affiliation: 
• Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark.
State Key Laboratory of Agricultural and Forestry Biosecurity, College of Plant Protection, Nanjing Agricultural University, Nanjing, China.
The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China.
INRAE, Aix Marseille Univ, UMR 1163 Biodiversité et Biotechnologie Fongiques (BBF), Marseille, France.
INRAE, Aix Marseille Univ, 3PE Platform, Marseille, France.
INRAE, UR1268 Biopolymères Interactions Assemblages (BIA), Nantes, France.
INRAE, PROBE research infrastructure, BIBS Facility, Nantes, France.
Department of Chemistry, Technical University of Denmark, Lyngby, Denmark.
State Key Laboratory of Agricultural and Forestry Biosecurity, College of Plant Protection, Nanjing Agricultural University, Nanjing, China. [e-mail].
The Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China. [e-mail].
Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 41.15 kDa 
• Atom Count: 3,168 
• Modeled Residue Count: 346 
• Deposited Residue Count: 366 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mucin-like protein	A, B	183	Phytophthora sojae	Mutation(s): 0  Gene Names: PHYSODRAFT_483955
UniProt
Find proteins for G4YSM3 (Phytophthora sojae (strain P6497)) Explore G4YSM3  Go to UniProtKB:  G4YSM3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)	D [auth A], I [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N
EDO	C [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.79 Å
• R-Value Free:  0.202 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.161 (Depositor), 0.172 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.267	α = 90
b = 73.129	β = 90
c = 116.418	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
AutoProcess	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-03-12 
Deposition Author(s): Banerjee, S., Turella, S., Morth, J.P., Abou Hachem, M.

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Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF20OC0064747

Revision History  

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