Computational comparison of β-mannosidases of animals, humans, microbes, and plants

The b-mannosidase (MANB) enzyme is involved in removing mannose residue from the nonreducing end, and its impaired activity leads to b-mannosidosis. MANB amino acid sequences of humans, other mammals, plants, fungi, and bacteria were compared to determine their similarities, differences, and predicted 3D structures. Our cloned MANB DNA sequence showed a 99% similarity to a previously reported human MANB DNA sequence but 16 nucleotide differences were observed, showing the polymorphic nature of the enzyme. The 9 changed codons coded the different amino acids Ile, Lys, Ile, Thr, Arg, Leu, Leu, Gly, and Asp, while 7 changed codons coded the same amino acids, Ile, Arg, Gln, Val, Ile, Pro, and Val. The amino acid sequence comparison of human MANB with bovine, goat, and mouse MANB showed a nearly 75% similarity, while 10%-13%, 17%-18%, and 9%-23% similarities were observed with plant, fungi, and bacteria MANB, respectively. The catalytic nucleophilic and proton donor sites were conserved in the /beta-mannosidase of mammals, plants, fungi, and bacteria, except L. esculentum, and the nucleophilic site of P. furiosus was also changed. The catalytic sites of MANB indicated that it follows a dyad catalytic mechanism. Additionally, 2 common putative glycosylation sites at N-residues 35 and 77 were conserved. The 3D structure prediction indicated differences in the α-helix loop, while the b-pleated sheets were nearly the same. The comparison showed that the MANB enzyme is polymorphic in nature with conserved catalytic sites and has an evolutionary relationship among different species. The 3D structure comparison of MANB will be helpful to understand the disease process of b-mannosidosis.

Anahtar Kelimeler:

DNA sequence, amino acid comparison, computational analysis, β-Mannosidase

Computational comparison of β-mannosidases of animals, humans, microbes, and plants

Keywords:

Key words: b-Mannosidase, DNA sequence, amino acid comparison, computational analysis,

PDF

___

Ademark, P., Lundqvist, J., Hagglund, P., Tenkanen, M., Torto, N., Tjerneld, F., Stalbrand, H.: Hydrolytic properties of a beta- mannosidase purifi ed from Aspergillus niger. J. Biotechnol., 1999; 75: 281-289. 2. Jones, M.Z., Rathke, E.J., Gage, D.A., Costello, C.E., Murakami, K., Ohta, M., Matsuura, F.: Oligosaccharides accumulated in the bovine beta-mannosidosis kidney. J. Inherit. Metab. Dis., 1992; 15: 57-67.
Sopher, B.L., Traviss, C.E., Cavanagh, K.T., Jones, M.Z., Friderici, K.H.: Bovine kidney beta-mannosidase: purifi cation and characterization. Biochem. J., 1983; 289: 343-347.
Percheron, F., Foglietti, M.J., Bernard, M., Ricard, B.: Mammalian beta-D-mannosidase and beta-mannosidosis. Biochimie, 1992; 74: 5-11.
Kurakake, M., Komaki, T.: Production of beta-mannanase and beta-mannosidase from Aspergillus awamori K4 and their properties. Curr. Microbiol., 2001; 42: 377-380.
Duff aud, G.D., McCutchen, C.M., Leduc, P., Parker, K.N., Kelly, R.M.: Purifi cation and characterization of extremely thermostable beta-mannanase, beta-mannosidase, and alpha- galactosidase from the hyperthermophilic eubacterium Th ermotoga neapolitana 5068. Appl. Environ. Microbiol., 1997; 63: 169-177.
Bauer, M.W., Bylina, E.J., Swanson, R.V., Kelly, R.M.: Comparison of a beta-glucosidase and a beta-mannosidase from the hyperthermophilic archaeon Pyrococcus furiosus. Purifi cation, characterization, gene cloning, and sequence analysis. J. Biol. Chem., 1996; 271: 23749-23755. 8. Mo, B., Bewley, J.D.: Beta-mannosidase (EC 3.2.1.25) activity during and following germination of tomato (Lycopersicon esculentum Mill.) seeds. Purifi characterization. Planta, 2002; 215: 141-152. cation, cloning and
Ishimizu, T., Sasaki, A., Okutani, S., Meada, M., Yamagishi, M., Hase, S.: Endo-beta-mannosidase, a plant enzyme acting on N-Glycan. Purifi cation, molecular cloning and characterization. J. Biol. Chem., 2004; 279: 38555-38562.
Pearce, R.D., Callahan, J.W., Novak, A., Little, P.B., Clarke, J.T.: Properties of partially purifi ed goat kidney beta-D- mannosidase. Br. Vet. J., 1990; 146: 270-280.
Guadalupi, R., Bernard, M., Orlacchio, A., Foglietti, M.J., Emiliani, C.: Purifi cation and properties of human urinary beta-D-mannosidase. Biochem. Biophys. Acta, 1996: 1293; 9-16.
Jones, M.Z., Cunningham, J.G., Dade, A.W., Alessi, D.M., Mostosky, U.V., Vorro, J.R., Benitez, J.T., Lovell, K.L.: Caprine beta-mannosidosis: clinical and pathological features. J. Neuropathol. Exp. Neurol., 1983; 42: 268-285.
Jolly, R.D., Th ompson, K.G., Bayliss, S.L., Vidler, B.M., Healy, P.J.: beta-Mannosidosis in a Salers calf: a new storage disease of cattle. N.Z. Vet. J., 1990; 38: 102-105.
Levade, T., Graber, D., Flurin, V., Delisle, M.B., Pieraggi, M.T., Testut, M.F., Carriere, J.P., Salvayre, R.: Human beta- mannosidase defi ciency associated with peripheral neuropathy. Ann. Neurol., 1994; 35: 116-119.
Alkhayat, A.H., Kraemer, S.A., Leipprandt, J.R., Macek, M., Kleijer, W.J., Friderici, K.H.: Human beta-mannosidase cDNA characterization and fi rst identifi cation of a mutation associated with human beta-mannosidosis. Hum. Mol. Genet., 1998; 7: 75-83.
Bryan, L., Schmutz, S., Hodges, S.D., Snyder, F.F.: Bovine beta- mannosidase defi ciency. Biochem. Biophys. Res. Commun., 1990; 173: 491-495.
Lovell, K.L., Kranich, R.J., Cavanagh, K.T.: Biochemical and histochemical analysis of lysosomal enzyme activities in caprine beta-mannosidosis. Mol. Chem. Neuropathol., 1994; 21: 61-74.
Uchino, Y., Fukushige, T., Yotsumoto, S., Hashiguchi, T., Taguchi, H., Suzuki, N., Konohana, I., Kanzak, T.: Morphological and biochemical studies of human beta- mannosidosis: identifi cation of a novel beta-mannosidase gene mutation. Br. J. Dermatol., 2003; 149: 23-29.
Sedel, F., Friderici, K., Nummy, K., Caillaud, C., Chabli, A., Durr, A., Lubetzki, C., Agid, Y.: Atypical Gilles de la Tourette Syndrome with beta-mannosidase defi ciency. Arch. Neuro., 2006; 63: 129-131.
Poenaru, L., Akli, S., Rocchiccioli, F., Eydoux, P., Zamet, P.: Human beta-mannosidosis: a 3-year-old boy with speech impairment and emotional instability. Clin. Genet., 1992; 41: 331-334.
Cooper, A., Wraith, J.E., Savage, W.J., Th ornley, M., Noronha, M.J.: Beta-mannosidase defi ciency in a female infant with epileptic encephalopathy. J. Inherit. Metab. Dis., 1991; 14: 18- 22.
Rodriguez-Serna, M., Botella-Estrada, R., Chabas, A., Coll, M.J., Oliver, V., Febrer, M.I., Aliaga, A.: Angiokeratoma corporis diff usum associated with beta-mannosidase defi ciency. Arch. Dermatol. 1996; 132: 1219-1222.
Kozak, M.: Compilation and analysis of sequence upstream from the translation start site in eukaryotic mRNA. Nucleic Acid Res., 1984; 12: 857-872.
von Heijne, G. A new method for predicting signal sequence cleavage site. Nucleic Acid Res., 1986; 14: 4683-4690.
Kyte, J., Doolittle, R.: A simple method for displaying the hydropathic character of a protein. J. Mol. Biol., 1982; 157: 105- 132.
Berman, H., Henrick, K., Nakamura, H., Markley, J.L.: Th e worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acid Res. 2007; 35: D301-D303.
Wu, C.H., Apweiler, R., Bairoch, A., Natale, D.A., Barker, W.C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M.J., Mazumder, R., O’Donovan, C., Redaschi, N., Suzek, B. Th e Universal Protein Resource (Uniport): an expanding universe of protein information. Nucleic Acid Res., 2006; 34: D187-D189.
Mizuguchi, K., Deane, C.M., Blundell, T.L., Overington, J.P.: HOMSTRAD: a database of protein structure alignments for homologous families. Protein Sci. 1998; 7: 2469-2471.