title: Bioinformatics characterization of potential new beta-glucuronidase from Streptococcus equi subsp. zooepidemicus.
abstract: Recently, the gene coding for a new beta-glucuronidase enzyme has been identified and cloned from Streptococcus equi subsp. zooepidemicus. This is another report of a beta-glucuronidase gene cloned from bacterial species. The ORF Finder analysis of a sequenced DNA (EMBL, AJ890474) revealed a presence of 1,785 bp large ORF potentially coding for a 594 aa protein. Three protein families in (Pfam) domains were identified using the Conserved Domain Database (CDD) analysis: Pfam 02836, glycosyl hydrolases family 2, triose phosphate isomerase (TIM) barrel domain; Pfam 02837, glycosyl hydrolases family 2, sugar binding domain; and Pfam 00703, glycosyl hydrolases family 2, immunoglobulin-like beta-sandwich domain. To gain more insight into the enzymatic activity, the domains were used to generate a bootstrapped unrooted distance tree using ClustalX. The calculated distances for two domains, TIM barrel domain, and sugar-binding domain were comparable and exhibited similarity pattern based on function and thus being in accordance with recently published works confirming beta-glucuronidase activity of the enzyme. The calculated distances and the tree arrangement in the case of centrally positioned immonoglobulin-like beta-sandwich domain were somewhat higher when compared to other two domains but clustering with other beta-glucuronidases was rather clear. Nine proteins, including beta-glucuronidases, beta-galactosidase, and mannosidase were selected for multiple alignment and subsequent distance tree creation.
authors.affiliation: CPN spol sro, Dolní Dobrouc, Czech Republic. krahulec@contipro.cz
authors.forename: Ján
authors.initials: J
authors.lastname: Krahulec
authors.forename: Tomás
authors.initials: T
authors.lastname: Szemes
authors.forename: Jana
authors.initials: J
authors.lastname: Krahulcová
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D016000:Cluster Analysis; D019295:Computational Biology; D005966:Glucuronidase / Q000235:genetics*; D006736:Horses; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary / Q000235:genetics; D017422:Sequence Analysis, DNA; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid; D018502:Streptococcus equi / Q000235:genetics*
chemical_list: D005966:Glucuronidase