PDBsum entry 5yjs

Plant protein

PDB id: 5yjs

Contents

Protein chains

370 a.a.

Ligands

SAL ×2

PG4

Metals

CU1 ×2

_CL

_NA

Waters ×324

PDB id:

5yjs

Name:

Plant protein

Title:

Structure of vicilin from capsicum annuum

Structure:

Vicilin-like antimicrobial peptides 2-2. Chain: a, b. Synonym: bell pepper

Source:

Capsicum annuum. Organism_taxid: 4072

Resolution:

2.16Å R-factor: 0.177 R-free: 0.217

Authors:

M.Shikhi,D.T.Nair,D.M.Salunke

Key ref:

M.Shikhi et al. (2018). Structure-guided identification of function: role of Capsicum annuum vicilin during oxidative stress. Biochem J, 475, 3057-3071. PubMed id: 30181145 DOI: 10.1042/BCJ20180520

Date:

11-Oct-17 Release date: 10-Oct-18

Protein chains

A0A452CSM5  (A0A452CSM5_CAPAN) -  Vicilin-like antimicrobial peptides 2-2 from Capsicum annuum

Seq: 390 a.a.

Struc: 370 a.a.

DOI no: 10.1042/BCJ20180520

Biochem J 475:3057-3071 (2018)

PubMed id: 30181145

Structure-guided identification of function: role of Capsicum annuum vicilin during oxidative stress.

M.Shikhi, D.T.Nair, D.M.Salunke.

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 Capsicum annuum - 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.