The crystal structure of PGIP (polygalacturonase inhibiting protein), a leucine rich repeat protein involved in plant defense

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.190 

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The Crystal Structure of Polygalacturonase-Inhibiting Protein (Pgip), a Leucine-Rich Repeat Protein Involved in Plant Defense

Di Matteo, A.Federici, L.Mattei, B.Salvi, G.Johnson, K.A.Savino, C.De Lorenzo, G.Tsernoglou, D.Cervone, F.

(2003) Proc Natl Acad Sci U S A 100: 10124

  • DOI: https://doi.org/10.1073/pnas.1733690100
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Polygalacturonase-inhibiting proteins (PGIPs) are plant cell wall proteins that protect plants from fungal invasion. They interact with endopolygalacturonases secreted by phytopathogenic fungi, inhibit their enzymatic activity, and favor the accumulation of oligogalacturonides, which activate plant defense responses. PGIPs are members of the leucine-rich repeat (LRR) protein family that in plants play crucial roles in development, defense against pathogens, and recognition of beneficial microbes. Here we report the crystal structure at 1.7-A resolution of a PGIP from Phaseolus vulgaris. The structure is characterized by the presence of two beta-sheets instead of the single one originally predicted by modeling studies. The structure also reveals a negatively charged surface on the LRR concave face, likely involved in binding polygalacturonases. The structural information on PGIP provides a basis for designing more efficient inhibitors for plant protection.

  • Organizational Affiliation

    Department of Biochemical Sciences and Consiglio Nazionale delle Ricerche, Institute for Molecular Biology and Pathology, University of Rome La Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
POLYGALACTURONASE INHIBITING PROTEIN313Phaseolus vulgarisMutation(s): 0 
Find proteins for P58822 (Phaseolus vulgaris)
Explore P58822 
Go to UniProtKB:  P58822
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP58822
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.190 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.84α = 90
b = 65.45β = 90
c = 34.64γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-24
    Type: Initial release
  • Version 1.1: 2012-01-25
    Changes: Derived calculations, Non-polymer description, Other, Version format compliance
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Other, Structure summary