Functional and Structural Analysis of Carbohydrate-binding Module of Eukaryotic α-L-rhamnosidase
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Abstract:
The analyses of the physicochemical properties and the construction of the phylogenetic tree for the eukaryotic α-L-rhamnosidase CBM were performed using ExPASy website and MEGA 6.0 software, in order to analyze the function of CBM in the CBM67 family of eukaryotic α-L-rhamnosidase located in the CAZy database. It was found that the eukaryotic α-L-rhamnosidase CBM can be divided into three major classes, and most are hydrophobic proteins, with the number of amino acids in the range of 239~377, molecular weight (Mr) in the range of 24540.58~40740.16 u, isoelectric point (pI) in the range of 3.93~8.74, total number of negatively charged residues in the range of 20~29, total number of positively charged residues in the range of 6~33, total number of atoms in the range of 3415~5712, and average hydrophilicity coefficient in the range of -0.077~0.377. The amino acid region of the eukaryotic α-L-rhamnosidase CBM in the CBM67 family was determined by sequence alignment analysis using the ClustalX 2.0 program and the Espript website. Using the Discovery Studio 2019 software for homology modeling and molecular docking, the three-dimensional structure of α-L-rhamnosidase CBM consisting of 12 β-sheets was constructed. The molecular docking with L-rhamnose revealed that CBM could recognize substrates through producing strong hydrogen bonds and van der Waals forces with L-rhamnose, to promote the occurrence of enzymatic hydrolysis. These results will help us understand better the structural basis and common approaches for CBM to recognize and bind to the substrate, thus, provide theoretical guidance for improving the binding of CBM.