Abstract Details

Poster 40: Building of 3D Structure Model and Annotation of Bifidobacterial Beta-galactosidase

Vladimir Vukic1, Dajana Hrnjez1, Spasenija Milanovic1, Mirela Ilicic1, Katarina Kanuric1
1University of Novi Sad, Faculty of Technology, Bulevar Cara Lazara 1, Republic of Serbia
Bifidobacteria represent one of the most numerous groups of probiotic bacteria that have beneficial effects on human health (especially on their digestive tract), which are widely used as commercial probiotic starter culture. Bifidobacterium animalis ssp. lactis BB12 is one of the commercial strains. Recently, its genome was completely sequenced, which allowed detailed genomic analysis including gene annotation, gene ontology, structural analysis, etc. Beta-galactosidase is the essential enzyme in fermented dairy technology. It is involved in the first reaction in lactose fermentation (hydrolyses lactose on glucose and galactose), which results in lactic acid production.
The aim of this research was to determine 3D structure model of the beta-galactosidase from Bifidobacterium animalis ssp. lactis BB12, its potential active sites, ligands and to include them in the 3D model.
Blast program was used for sequence similarities search. 3D structure of beta-galactosidase, was modelled using Modeller software. Sequence annotation, which included active and binding sites, was performed using UniProt database. Modelling of potential ligands was performed using Site Engine program. Parallel analysis for ligand binding site verification was performed using 3DLigandSite Ligand binding site prediction Server, Structural bioinformatics group, Imperial College, London. Conserved domen analysis was done by VASTA program.
Phylogenetic analysis and data bases of experimental 3D structure results revealed that constructed model of beta-galactosidase is closely related and has most similarities with beta-galactosidase from Bacillus circulans ssp. alkalophilus, with E value = 1e-119 and Thermus thermophillus with E value = 2e-65. Although beta-galactosidase from these species are closely related (small E value), species are not closely related and are classified in different phylum. These results indicate high conservation and essential role of the beta-galactosidase in their metabolism. In order to find functional sites three conserved domens were obtained, which was used for ligand binding sites prediction. The most probable ligands are alpha D-galactose and zinc ion. These results showed (as it is expected) that modelled protein is carbohydrase. In addition it is a metal binding carbohydrase. Protein domain which belongs to glycosil hydrolase 42 families is located at C terminal end and binds alpha D-galactose. Quaternary structure prediction model revealed that Bifidobacterium animalis ssp. lactis BB12 beta-galactosidase consists of six protein subunits coded by the same gene. Enzyme's subunits are organized in the way that Zn ions are positioned in the center of the enzyme.

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