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Doctoral thesis, 2010

Structural studies of sugar binding proteins

Sooriyaarachchi, Sanjeewani

Abstract

Binding proteins, which are themselves non-enzymatic, play an important role in enzymatic reactions as well as non-enzymatic processes by providing a binding platform for the specific recognition of particular molecules. For example, periplasmic binding proteins play a vital role in nutrient uptake in Gram-negative bacteria. In the present study, three sugar binding proteins, including two periplasmic binding proteins and a β-glucan binding protein, are described. The glucose/galactose binding protein in complex with (2R)-glyceryl-β-D-galactopyranoside, another physiologically relevant ligand for the protein, was revealed. The structure was solved using the molecular replacement method and refined to 1.87 Å with R and R free values 17% and 22%. The structure displays the closest form among the available glucose/galactose binding protein structures with three additional binding residues, which are conserved among the group. We also present three different conformations of E. coli xylose binding protein structures, open ligand free, open liganded and closed liganded. This is the first structure of the open liganded form in the pentose/hexose sugar-binding cluster. The structures were solved using molecular replacement method and refined to 2.15 Å, 2.1 Å and to 2.2 Å respectively. The new family of antimicrobial protein, secreted upon fungal attacks from Pinus sylvestris was present here with the binding and activity assays. The inhibition of vegetative growth and the spore germination of the causative agent of the disease, root and butt rot was proved with low concentrations of the peptide. The assays determined its ability to bind with β-(1,3)-D-glucans. The homology model was made using the PDB structure 1C01, the antimicrobial protein from Macadamia integrifolia, which has 64% sequence identity.

Keywords

binding proteins; xylose; glucans; models; x rays

Published in

Acta Universitatis Agriculturae Sueciae
2010, number: 2010:28
ISBN: 978-91-576-7505-7
Publisher: Dept. of Molecular Biology, Swedish University of Agricultural Sciences

Authors' information

Sooriyaarachchi, Sanjeewani
Swedish University of Agricultural Sciences, Department of Molecular Biology

UKÄ Subject classification

Biochemistry and Molecular Biology
Structural Biology

URI (permanent link to this page)

https://res.slu.se/id/publ/29408