8IKX | pdb_00008ikx

An Arabidopsis polygalacturonase PGLR

• PDB DOI: https://doi.org/10.2210/pdb8IKX/pdb

• Classification: HYDROLASE
• Organism(s): Arabidopsis thaliana
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2023-03-01 Released: 2024-02-07 
• Deposition Author(s): Xiao, Y., Chai, J.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.179 (Depositor), 0.179 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.158 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

A plant mechanism of hijacking pathogen virulence factors to trigger innate immunity.

Xiao, Y., Sun, G., Yu, Q., Gao, T., Zhu, Q., Wang, R., Huang, S., Han, Z., Cervone, F., Yin, H., Qi, T., Wang, Y., Chai, J.

(2024) Science 383: 732-739

• PubMed: 38359129 
• DOI: https://doi.org/10.1126/science.adj9529
• Primary Citation Related Structures: 
  8IKW, 8IKX


• PubMed Abstract: 
  

  Polygalacturonase-inhibiting proteins (PGIPs) interact with pathogen-derived polygalacturonases to inhibit their virulence-associated plant cell wall-degrading activity but stimulate immunity-inducing oligogalacturonide production. Here we show that interaction between Phaseolus vulgaris PGIP2 (PvPGIP2) and Fusarium phyllophilum polygalacturonase (FpPG) enhances substrate binding, resulting in inhibition of the enzyme activity of FpPG. This interaction promotes FpPG-catalyzed production of long-chain immunoactive oligogalacturonides, while diminishing immunosuppressive short oligogalacturonides. PvPGIP2 binding creates a substrate binding site on PvPGIP2-FpPG, forming a new polygalacturonase with boosted substrate binding activity and altered substrate preference. Structure-based engineering converts a putative PGIP that initially lacks FpPG-binding activity into an effective FpPG-interacting protein. These findings unveil a mechanism for plants to transform pathogen virulence activity into a defense trigger and provide proof of principle for engineering PGIPs with broader specificity.

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Organizational Affiliation: 
• Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China.
Department of Plant Pathology, Nanjing Agricultural University, Nanjing 210095, China.
Key Laboratory of Soybean Disease and Pest Control (Ministry of Agriculture and Rural Affairs), Nanjing Agricultural University, Nanjing 210095, China.
The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing 210095, China.
School of Life Sciences, Westlake University, Hangzhou 310024, China.
Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou 310024, Zhejiang, China.
Dipartimento di Biologia e Biotecnologie "C. Darwin," Sapienza, University of Rome, Piazzale Aldo Moro, 00185 Roma, Italy.
Dalian Engineering Research Center for Carbohydrate Agricultural Preparations, Liaoning Provincial Key Laboratory of Carbohydrates, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 42.99 kDa 
• Atom Count: 3,501 
• Modeled Residue Count: 390 
• Deposited Residue Count: 390 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pectin lyase-like superfamily protein	A	390	Arabidopsis thaliana	Mutation(s): 0  Gene Names: At5g14650, AT5G14650, T15N1.140, T15N1_140
UniProt
Find proteins for Q9LYJ5 (Arabidopsis thaliana) Explore Q9LYJ5  Go to UniProtKB:  Q9LYJ5
Glycosylation
Glycosylation Sites: 2

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	7		N-Glycosylation
Glycosylation Resources
GlyTouCan: G55220VL GlyCosmos: G55220VL GlyGen: G55220VL

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	C [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.179 (Depositor), 0.179 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.158 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.212	α = 94.59
b = 43.54	β = 99.99
c = 63.478	γ = 110.55

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-02-07 
Deposition Author(s): Xiao, Y., Chai, J.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2024-02-07
  Type: Initial release
  
• Version 1.1: 2024-02-28
  Changes: Database references
• Version 1.2: 2024-10-30
  Changes: Structure summary