COMPUTATIONAL STRUCTURAL AND FUNCTIONAL PROTEOMICS THE ALPHA-GALACTOSIDASE SUPERFAMILY: SEQUENCE BASED CLASSIFICATION OF ALPHA-GALACTOSIDASES AND RELATED GLYCOSIDASES Naumoff D.G. State Institute for Genetics and Selection of Industrial Microorganisms, Moscow, Russia, e-mail:
[email protected] Keywords: α-galactosidase, melibiase, glycoside hydrolase, GH-D clan, GH31 family, GHX family, COG1649, enzyme classification, protein family, protein phylogeny Summary Motivation: About 1 % of genes in genomes code enzymes with glycosidase activities. On the basis of sequence similarity all known glycosidases have been classified into 90 families. In many cases proteins of different families have common evolution origin. It makes necessary to combine the corresponding families into a superfamily. Results: Using of the PSI-BLAST program we found significant sequence similarity of several glycosidase families, two of which includes enzymes with the α galactosidase activity. Sequence homology, common catalytic mechanism, folding similarities, and composition of the active center allowed us to group three of these families – GH27, GH31, and GH36 – into the α-galactosidase superfamily. Phylogenetic analysis of this superfamily revealed polyphyletic origin of GH36 family, which could be divided into four families. Glycosidases of the α-galactosidase superfamily have a distant relationship with proteins belonging to families GH13, GH70, and GH77 of glycosidases, as well as with two families of predicted glycosidases. Introduction Glycoside hydrolases or glycosidases (EC 3.2.1.-) are a widespread group of enzymes, hydrolyzing the glycosidic bonds between two carbohydrates or between a carbohydrate and an aglycone moiety. A large multiplicity of these enzymes is a consequence of the extensive variety of their natural substrates: di-, oligo-, and polysaccharides.