We found endo-␣-N-acetylgalactosaminidase in most bifidobacterial strains, which are predominant bacteria in the human colon. This enzyme catalyzes the liberation of galactosyl 1,3-N-acetyl-Dgalactosamine (Gal1,3GalNAc) ␣-linked to serine or threonine residues from mucin-type glycoproteins. The gene (engBF) encoding the enzyme has been cloned from Bifidobacterium longum JCM 1217. The protein consisted of 1,966 amino acid residues, and the central domain (590 -1381 amino acid residues) exhibited 31-53% identity to hypothetical proteins of several bacteria including Clostridium perfringens and Streptococcus pneumoniae. The recombinant protein expressed in Escherichia coli liberated Gal1,3GalNAc disaccharide from Gal1,3GalNAc␣1pNP and asialofetuin, but did not release GalNAc, Gal1,3(GlcNAc1,6)GalNAc, GlcNAc1,3GalNAc, and Gal1,3GlcNAc from each p-nitrophenyl (pNP) substrate, and also did not release sialo-oligosaccharides from fetuin, indicating its strict substrate specificity for the Core 1-type structure. The stereochemical course of hydrolysis was determined by 1 H NMR and was found to be retention. Site-directed mutagenesis of a total of 22 conserved Asp and Glu residues suggested that Asp-682 and Asp-789 are critical residues for the catalytic activity of the enzyme. The enzyme also exhibited transglycosylation activity toward various mono-and disaccharides and 1-alkanols, demonstrating its potential to synthesize neoglycoconjugates. This is the first report for the isolation of a gene encoding endo-␣-N-acetylgalactosaminidase from any organisms and for the establishment of a new glycoside hydrolase family (GH family 101).Mucin-type oligosaccharides (O-glycans) are involved in several important biological events including cell-to-cell communication in higher eukaryotes, bacterial adhesion to host cells, and so on (1). Eight core-type structures of O-glycans have been proposed, and among them, galactosyl 1,3-N-acetyl-D-galactosamine (Gal1,3GalNAc) 2 attached to the serine or threonine residue via an ␣-linkage (Core 1, also referred to as T antigen) is one of the most abundant core structures found in mucin glycoproteins that are widely distributed in intestinal tracts of human and animals. This immunogenic structure is normally masked by further glycosylation such as sialylation (sialyl T antigen) and N-acetylglucosaminylation (Core 2 structure). However, it has been shown that T antigen is frequently exposed on the cell surface of carcinoma and T-cell lymphoma, and this unmasked form is thought to be involved in tumor cell adhesion and tissue invasion (2, 3). In addition, incomplete synthesis of the Core 1 structure associates with several autoimmune diseases including IgA nephropathy (4), Tn-syndrome (5), and Henoch-Schönlein purpura (6).Endo-␣-N-acetylgalactosaminidase (EC 3.2.1.97; endo-␣-GalNAcase, glycopeptide ␣-N-acetylgalactosaminidase) is a unique enzyme that hydrolyzes Core 1-type O-glycan from glycoproteins. This enzyme also serves as a powerful tool for elucidating the presence of O-glycan...