5CAD

Crystal structure of the vicilin from Solanum melongena revealed existence of different anionic ligands in structurally similar pockets

Summary for 5CAD

• Entry DOI: 10.2210/pdb5cad/pdb
• Descriptor: SM80.1 Vicilin, MAGNESIUM ION, ACETATE ION, ... (5 entities in total)
• Functional Keywords: solanaceae; solanum melongena;7s vicilin; sm80.1, plant protein
• Biological source: Solanum melongena (eggplant)
• Total number of polymer chains: 1
• Total formula weight: 42856.05

Authors

Jain, A.,Kumar, A.,Salunke, D.M. (deposition date: 2015-06-29, release date: 2016-04-06, Last modification date: 2024-03-20)

Primary citation

Jain, A.,Kumar, A.,Salunke, D.M.
Crystal structure of the vicilin from Solanum melongena reveals existence of different anionic ligands in structurally similar pockets
Sci Rep, 6:23600-23600, 2016

PubMed Abstract: Crystal structure of a vicilin, SM80.1, was determined towards exploring its possible physiological functions. The protein was purified from Solanum melongena by combination of ammonium sulphate fractionation and size exclusion chromatography. Structure was determined ab initio at resolution of 1.5 Å by X-ray crystallography showing the three-dimensional topology of the trimeric protein. Each monomer of SM80.1 consists of two similar domains with hydrophobic binding pocket and each accommodating different ligands, i.e. acetate and pyroglutamate. The relatively high stability of these independent anionic ligands in similar pockets indicated a strict requirement of stabilization by hydrogen bonds with the charged residues, suggesting a degree of plasticity within the binding pocket. Comparison of SM80.1 structure with those of other 7S vicilins indicated conservation of putative binding pocket for anionic ligands. Here we propose the possibility of trapping of these ligands in the protein for their requirement in the metabolic processes.

PubMed: 27004988
DOI: 10.1038/srep23600

Experimental method

X-RAY DIFFRACTION (1.49 Å)