1OGQ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.190 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 10.1073/pnas.1733690100
  • Primary Citation of Related Structures:  
    1OGQ

  • 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
POLYGALACTURONASE INHIBITING PROTEINA313Phaseolus vulgarisMutation(s): 0 
Gene Names: PGIP2
Find proteins for P58822 (Phaseolus vulgaris)
Explore P58822 
Go to UniProtKB:  P58822
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
B [auth A], C [auth A], D [auth A], E [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
F [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report



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