title: Molecular phylogeny and predicted 3D structure of plant beta-D-N-acetylhexosaminidase.
abstract: beta-D-N-Acetylhexosaminidase, a family 20 glycosyl hydrolase, catalyzes the removal of β-1,4-linked N-acetylhexosamine residues from oligosaccharides and their conjugates. We constructed phylogenetic tree of β-hexosaminidases to analyze the evolutionary history and predicted functions of plant hexosaminidases. Phylogenetic analysis reveals the complex history of evolution of plant β-hexosaminidase that can be described by gene duplication events. The 3D structure of tomato β-hexosaminidase (β-Hex-Sl) was predicted by homology modeling using 1now as a template. Structural conformity studies of the best fit model showed that more than 98% of the residues lie inside the favoured and allowed regions where only 0.9% lie in the unfavourable region. Predicted 3D structure contains 531 amino acids residues with glycosyl hydrolase20b domain-I and glycosyl hydrolase20 superfamily domain-II including the (β/α)8 barrel in the central part. The α and β contents of the modeled structure were found to be 33.3% and 12.2%, respectively. Eleven amino acids were found to be involved in ligand-binding site; Asp(330) and Glu(331) could play important roles in enzyme-catalyzed reactions. The predicted model provides a structural framework that can act as a guide to develop a hypothesis for β-Hex-Sl mutagenesis experiments for exploring the functions of this class of enzymes in plant kingdom.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi 6205, Bangladesh ; Genetic Engineering Laboratory, Department of Molecular Biology, Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia.
authors.forename: Md Anowar
authors.initials: MA
authors.lastname: Hossain
authors.affiliation: Genetic Engineering Laboratory, Department of Molecular Biology, Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia.
authors.forename: Hairul Azman
authors.identifier: 0000-0002-6700-6138
authors.initials: HA
authors.lastname: Roslan
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D019295:Computational Biology; D030561:Databases, Nucleic Acid; D019143:Evolution, Molecular; D020440:Gene Duplication; D016013:Likelihood Functions; D018551:Solanum lycopersicum / Q000201:enzymology*; D008957:Models, Genetic; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D011487:Protein Conformation; D016415:Sequence Alignment; D013045:Species Specificity; D001619:beta-N-Acetylhexosaminidases / Q000737:chemistry* / Q000235:genetics*
chemical_list: D001619:beta-N-Acetylhexosaminidases