5YJS

Structure of vicilin from Capsicum annuum

Summary for 5YJS

• Entry DOI: 10.2210/pdb5yjs/pdb
• Descriptor: vicilin-like antimicrobial peptides 2-2, CHLORIDE ION, SODIUM ION, ... (7 entities in total)
• Functional Keywords: cupin, 7s globulin, copper site, binding pocket, plant protein
• Biological source: Capsicum annuum
• Total number of polymer chains: 2
• Total formula weight: 86369.44

Authors

Shikhi, M.,Nair, D.T.,Salunke, D.M. (deposition date: 2017-10-11, release date: 2018-10-10, Last modification date: 2023-11-22)

Primary citation

Shikhi, M.,Nair, D.T.,Salunke, D.M.
Structure-guided identification of function: role ofCapsicum annuumvicilin during oxidative stress.
Biochem. J., 475:3057-3071, 2018

PubMed Abstract: Proteins belonging to cupin superfamily are known to have critical and diverse physiological functions. However, 7S globulins family, which is also a part of cupin superfamily, were undermined as only seed storage proteins. Structure determination of native protein - Vic_CAPAN from was carried out, and its physiological functions were explored after purifying the protein by ammonium sulfate precipitation followed by size exclusion chromatography. The crystal structure of vicilin determined at 2.16 Å resolution revealed two monomers per asymmetric unit which are juxtaposed orthogonal with each other. Vic_CAPAN consists predominately of β-sheets that folds to form a β-barrel structure commonly called cupin fold. Each monomer of Vic_CAPAN consists of two cupin fold domains, N-terminal and C-terminal, which accommodate two different ligands. A bound ligand was identified at the C-terminal cupin fold in the site presumably conserved for metabolites in the crystal structure. The ligand was confirmed to be salicylic acid through mass spectrometric analysis. A copper-binding site was further observed near the conserved ligand-binding pocket, suggesting possible superoxide dismutase activity of Vic_CAPAN which was subsequently confirmed biochemically. Vicilins from other sources did not exhibit this activity indicating functional specificity of Vic_CAPAN. Discovery of bound salicylic acid, which is a known regulator of antioxidant pathway, and revelation of superoxide dismutase activity suggest that Vic_CAPAN has an important role during oxidative stress. As salicylic acid changes the redox state of cell, it may act as a downstream signal for various pathways involved in plant biotic and abiotic stress rescue.

PubMed: 30181145
DOI: 10.1042/BCJ20180520

Experimental method

X-RAY DIFFRACTION (2.16 Å)