We report here the molecular cloning, characterization, and catalytic mechanism of a novel glycosphingolipid-degrading -N-acetylgalactosaminidase (-NGA) from Paenibacillus sp. TS12 (NgaP). Consisting of 1034 putative amino acid residues, NgaP shares no sequence similarity with known proteins. Recombinant NgaP, expressed in Escherichia coli, cleaved the nonreducing terminal -GalNAc residues of gangliotriaosylceramide and globotetraosylceramide. The enzyme hydrolyzed para-nitrophenyl--N-acetylgalactosaminide ϳ100 times faster than para-nitrophenyl--N-acetylglucosaminide. GalNAc thiazoline, an analog of the oxazolinium intermediate and potent inhibitor for enzymes adopting substrate-assisted catalysis, competitively inhibited the enzyme. The K i of the enzyme for GalNAc thiazoline was 1.3 nM, whereas that for GlcNAc thiazoline was 46.8 M. Comparison of the secondary structure with those of known enzymes exhibiting substrate-assisted catalysis and point mutation analysis indicated that NgaP adopts substrate-assisted catalysis in which Glu-608 and Asp-607 could function as a proton donor and a stabilizer of the 2-acetamide group of the -GalNAc at the active site, respectively. These results clearly indicate that NgaP is a -NGA showing substrateassisted catalysis. This is the first report describing the molecular cloning of a -NGA adopting substrate-assisted catalysis.