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

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.

Fig. 1.

Structure of PGIP2 from P. vulgaris. (a) ribbon (21) representation of the structure of PGIP2. Sheets B1 and B2 are colored green, and helices are colored blue (light blue for the N-terminal α-helix and dark blue for 3₁₀-helices in the LRR central portion of the molecule). (b) Secondary structure organization of the LRR motif (residues 53–289) in PGIP2. The consensus sequence of PGIP2 and other plant-derived extracytoplasmic LRR (6) are shown together with the secondary structure elements found in PGIP2. Residues contributing to form the secondary structure elements are colored green (sheets B1 and B2) and blue (3₁₀-helix).

Fig. 2.

Backbone superposition of a single LRR motif of proteins representative of the LRR subfamilies defined by Kajava (23) with LRR6 of PGIP2 repeat (green). (a) Internalin B (25) (orange). (b) U2A′ (36) (dark pink). (c) Dynein LC1 (29) (light pink) belonging to the SDS22-like subfamily. (d) Skp2 (27) (light blue) belonging to the cysteine-containing subfamily. (e) YopM (26) (red) belonging to the bacterial subfamily. (f) RI (24) (dark blue) belonging to the RI-like subfamily. rms deviation (RMSD) values are calculated for the superposition of the first eight residues of each repeat forming the so-called β-structure + Asn-ladder region.

Fig. 3.

grasp (39) electrostatic potential surface of PGIP2. Regions of negative and positive potential are shown in red and blue, respectively. A wide negative pocket, putatively involved in PG recognition, is located in the middle of the inner concave surface of the protein. The residue Gln-224, crucial for PGIP2 specificity, is also indicated.