8S71 | pdb_00008s71

Oxidoreductase B from Phytophthora sojae

• PDB DOI: https://doi.org/10.2210/pdb8S71/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: 2.05 Å
• R-Value Free: 
  0.232 (Depositor), 0.233 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.177 (DCC) 

Starting Model: in silico

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 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: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 41.58 kDa 
• Atom Count: 3,057 
• Modeled Residue Count: 346 
• Deposited Residue Count: 370 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mucin-like protein	A, B	185	Phytophthora sojae	Mutation(s): 0  Gene Names: PHYSODRAFT_485524
UniProt
Find proteins for G4YSM7 (Phytophthora sojae (strain P6497)) Explore G4YSM7  Go to UniProtKB:  G4YSM7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CU (Subject of Investigation/LOI)	C [auth A], D [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.232 (Depositor), 0.233 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.177 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.067	α = 90
b = 106.897	β = 114.099
c = 44.815	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
TRUNCATE	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