International Summer School

   From Genome to Life:

    Structural, Functional and Evolutionary approaches



State Institute For Genetics And Selection of Industrial Microorganisms, Laboratory Of Bioinformatics, I-Dorozhny Proezd, 1, Moscow 113545, Russia

title: Sequence analysis and classification of alpha-galactosidases

Glycosyl hydrolases are a widespread group of enzymes that hydrolyze the glycosidic bonds between two carbohydrate residues. Currently, several thousand sequences of the proteins are known. They are grouped into 83 families on the basis of sequence similarity ( Four of these families (GH4, GH27, GH36, and GH57) include enzymes with alpha-galactosidase activity [E.C.]. GH4 and GH57 families encompass several types of glycosyl hydrolases. The alpha-galactosidase activity has been demonstrated only for three enzymes of GH4 family (from Escherichia coli, Thermotoga maritima, and T. neapolitana) and two enzymes of GH57 family (from Pyrococcus furiosus and Thermococcus alcaliphilus). The majority of known alpha-galactosidases belong to GH27 and GH36 families, which compose a superfamily (clan GH-D). We have performed sequence analysis of the two families. Most of GH27 sequences have a high level of sequence similarity (more than 30% of identical residues) and make up a distinct subfamily. Four main subgroups can be distinguished in this subfamily (> 50% of identical residues). One of them includes plant and Clostridium josui alpha-galactosidases and a hypothetical protein (ORF) from Streptomyces coelicolor. Other two subgroups comprise glycosidases from Ascomycota yeast and Vertebrata respectively. Some fungal alpha-galactosidases form the fourth subgroup. One of the Trichoderma reesei aipha-galactosidases, Arthrobacter globiformis isomaltodextranase, and Bacillus halodurans hypothetical protein along with two Arabidopsis thaliana hypothetical proteins are the most divergent representatives of GH27 family and can be considered the only known representatives of three other subfamilies. GH36 family is composed of two main subfamilies. Subfamily 36a includes alpha-galactosidases from Gram-positive bacteria, Absidia corymbifera, Aspergillus niger, Escherichia coli, and Trichoderma reesei as well as a hypothetical protein from Yersinia pestis. Subfamily 36b contains enzymes from Gram-negative bacteria (Proteobacteria, Thermotogales, and Thermus) and one hypothetical protein from Streptomyces coelicolor. Another hypothetical protein from St. coelicolor can be thought of as the only representative of the third subfamily. We will present data about homology of alpha-galactosidases from GH27 and GH36 families with glycosidases of GH31 family and proteins of aGalT family. The aGalT family is comprised of alpha-galactosyltransferases and seed imbibition proteins from higher plants, Bifidobacterium breve alpha-galactosidase, and hypothetical proteins from Sulfolobus solfataricus and Sul. tokodaii. We propose to include GH31 and aGalT families into the alpha-galactosidase superfamily, in addition to GH27 and GH36 families.