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Molecular phylogeny and predicted 3D structure of plant beta-D-N-acetylhexosaminidase.

Hossain MA, Roslan HA - ScientificWorldJournal (2014)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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.

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.

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Sequence alignment of β-Hex-Sl with nine other sequences by CD search. The amino acid residues Arg(178), Asp(207), His(261), Asp(330), Glu(331), Trp(378), Trp(404), Tyr(430), Asp(432), Trp(494), and Glu(496) were predicted to be responsible for the activity of β-Hex-S. The conserved amino acids are shown as yellow color.
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fig2: Sequence alignment of β-Hex-Sl with nine other sequences by CD search. The amino acid residues Arg(178), Asp(207), His(261), Asp(330), Glu(331), Trp(378), Trp(404), Tyr(430), Asp(432), Trp(494), and Glu(496) were predicted to be responsible for the activity of β-Hex-S. The conserved amino acids are shown as yellow color.

Mentions: The β-Hex-Sl protein sequence was analyzed by NCBI CD-search tool (CDD V3.0-44354 PSSMs) to identify the conserved domains (CD). The sequence contains a Glyco_hydro_20b (46~149 aa), GH20_HexA_HexB-like domain (167~549 aa), and a glycosyl hydrolase family 20, catalytic domain (167~522 aa) belongs to the GH20_hexosaminidase superfamily proteins (Figure 1). Based on CD database available and three-dimensional structure-activity relationship, the amino acid residues Arg(178), Asp(207), His(261), Asp(330), Glu(331), Trp(378), Trp(404), Tyr(430), Asp(432), Trp(494), and Glu(496) were predicted to be present in the active site of β-Hex-Sl with other sequences (Figure 2). The online tool NetNGlyc 1.0 server was used to identify the N-glycosylation site present in the protein sequence. The predicted N-glycosylation sites were position at 50 (NFTI), 86 (NLTS), 112 (NESY), 151 (NPTR), 299 (NPSI), 350 (NGTL), 362 (NNTL), 372 (NRTV), 390 (NPSL), 409 (NNTK), and 441 (NDSR) (data not shown). The software SignalP 4.1 server was used to predict the signal peptide cleavage site that was found to be in between positions 23 and 24 in the amino acid sequence.


Molecular phylogeny and predicted 3D structure of plant beta-D-N-acetylhexosaminidase.

Hossain MA, Roslan HA - ScientificWorldJournal (2014)

Sequence alignment of β-Hex-Sl with nine other sequences by CD search. The amino acid residues Arg(178), Asp(207), His(261), Asp(330), Glu(331), Trp(378), Trp(404), Tyr(430), Asp(432), Trp(494), and Glu(496) were predicted to be responsible for the activity of β-Hex-S. The conserved amino acids are shown as yellow color.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4129151&req=5

fig2: Sequence alignment of β-Hex-Sl with nine other sequences by CD search. The amino acid residues Arg(178), Asp(207), His(261), Asp(330), Glu(331), Trp(378), Trp(404), Tyr(430), Asp(432), Trp(494), and Glu(496) were predicted to be responsible for the activity of β-Hex-S. The conserved amino acids are shown as yellow color.
Mentions: The β-Hex-Sl protein sequence was analyzed by NCBI CD-search tool (CDD V3.0-44354 PSSMs) to identify the conserved domains (CD). The sequence contains a Glyco_hydro_20b (46~149 aa), GH20_HexA_HexB-like domain (167~549 aa), and a glycosyl hydrolase family 20, catalytic domain (167~522 aa) belongs to the GH20_hexosaminidase superfamily proteins (Figure 1). Based on CD database available and three-dimensional structure-activity relationship, the amino acid residues Arg(178), Asp(207), His(261), Asp(330), Glu(331), Trp(378), Trp(404), Tyr(430), Asp(432), Trp(494), and Glu(496) were predicted to be present in the active site of β-Hex-Sl with other sequences (Figure 2). The online tool NetNGlyc 1.0 server was used to identify the N-glycosylation site present in the protein sequence. The predicted N-glycosylation sites were position at 50 (NFTI), 86 (NLTS), 112 (NESY), 151 (NPTR), 299 (NPSI), 350 (NGTL), 362 (NNTL), 372 (NRTV), 390 (NPSL), 409 (NNTK), and 441 (NDSR) (data not shown). The software SignalP 4.1 server was used to predict the signal peptide cleavage site that was found to be in between positions 23 and 24 in the amino acid sequence.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

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.

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.

Show MeSH