Title: Molecular phylogeny, 3D-structural insights, docking and mechanisms of action of plant beta-galactosidases
Authors: Md. Anowar Hossain; Hairul Azman Roslan; Md. Rezaul Karim; Yoshinobu Kimura
Addresses: 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 ' Genetic Engineering Laboratory, Department of Molecular Biology, Faculty of Resource Science and Technology, Universiti Malaysia Sarawak, 94300 Kota Samarahan, Sarawak, Malaysia ' Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi 6205, Bangladesh ' Department of Biofunctional Chemistry, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan
Abstract: Beta-galactosidase (BGAL) is an exoglycosidase that catalyses the hydrolysis of terminal β-linked galactose residues. To better understand the molecular characteristics and structural insights of mango BGAL (MiBGAL), we performed the sequence analyses, reconstruction of the evolutionary tree, homology modelling and molecular docking. BGALs are widely distributed enzymes that evolved from a common bacterial ancestor. Plant BGALs (pBGALs) belong to glycosyl hydrolase-35(GH35) family and had close similarities with fungi BGALs. Three conserved motifs and GH35 putative active site with a consensus sequence G-G-P-[LIVM](2)-x(2)-Q-x-E-N-E-[FY] were identified in 67 BGAL sequences. Modelled 3D structure of MiBGAL is composed of a catalytic TIM barrel domain (domain-I) and three other β-domains, II, III & IV. Structural studies identified the residues Glu182 and Glu251 as the proton donor and nucleophile, respectively in pBGALs that could function through retaining mechanism. p-nitrophenyl-β-D-galactopyranoside and 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid could be potential substrate and inhibitor, respectively among the docked-ligands for both tomato BGAL4 and MiBGAL.
Keywords: plant beta-galactosidase; BGAL; phylogenetics; homology modelling; molecular docking; ligands; bioinformatics; 3D-structure; mango; tomato; fungi.
International Journal of Bioinformatics Research and Applications, 2016 Vol.12 No.2, pp.149 - 179
Received: 18 Sep 2015
Accepted: 06 Dec 2015
Published online: 21 Jun 2016 *