A computational approach to structural properties of glycoside hydrolase family 4 from bacteria.

Dana Craciun; Beatrice Vlad-Oros; Nicoleta Filimon; Vasile Ostafe; Adriana Isvoran

doi:10.18388/abp.2013_2020

Dana Craciun West University of Timisoara, Teacher Training Department, Timisoara, Romania.;
Beatrice Vlad-Oros West University of Timisoara, Department of Biology and Chemistry, Timisoara, Romania; Laboratory of Advanced Researches in Environmental Protection, Timisoara, Romania and University "Al. I. Cuza" from Lasi, Lasi, Romania (temporally affiliated).;
Nicoleta Filimon West University of Timisoara, Department of Biology and Chemistry, Timisoara, Romania and Laboratory of Advanced Researches in Environmental Protection, Timisoara, Romania.;
Vasile Ostafe West University of Timisoara, Department of Biology and Chemistry, Timisoara, Romania and Laboratory of Advanced Researches in Environmental Protection, Timisoara, Romania.;
Adriana Isvoran West University of Timisoara, Department of Biology and Chemistry, Timisoara, Romania and Laboratory of Advanced Researches in Environmental Protection, Timisoara, Romania.;

DOI: https://doi.org/10.18388/abp.2013_2020

Abstract

Structural bioinformatics approaches applied to the alpha- and beta-glycosidases from the GH4 enzyme family reveal that, despite low sequence identity, these enzymes possess quite similar global structural characteristics reflecting a common reaction mechanism. Locally, there are a few distinctive structural characteristics of GH4 alpha- and beta-glycosidases, namely, surface cavities with different geometric characteristics and two regions with highly dissimilar structural organizations and distinct physicochemical properties in the alpha- and beta-glucosidases from Thermotoga maritima. We suggest that these structurally dissimilar regions may be involved in specific protein-protein interactions and this hypothesis is sustained by the predicted distinct functional partners of the investigated proteins. Also, we predict that alpha- and beta-glycosidases from the GH4 enzyme family interact with difenoconazole, a fungicide, but there are different features of these interactions especially concerning the identified structurally distinct regions of the investigated proteins.