Corrigendum to “Structural Insights into the Substrate Specificity and Function of Escherichia coli K12 YgjK, a Glucosidase Belonging to the Glycoside Hydrolase Family 63” [J. Mol. Biol. 381 (2008) 116–128]

Structural Similarity between a Starch-hydrolyzing Enzyme and an N-Glycan-Hydrolyzing Enzyme: Exohydrolases Cleaving α-1,X-Glucosidic Linkages to Produce β-Glucose

“…(36); thus, the functions of bacterial GH63 proteins are unknown (9,37). We have reported the structure of E. coli YgjK, which was the first report on the crystal structure of a GH63 protein, and characterized its enzymatic properties (9). The domain compositions of E. coli YgjK and T. thermosaccharolyticum glucoamylase are essentially identical; they are composed of an N-terminal super β-sandwich domain and a C-terminal catalytic (α/α) 6 barrel domain, which joined by an α-helical linker.…”

“…Interestingly, E. coli YgjK showed high activity for the α-1,3-glucosidic linkage of nigerose (Glc-α-1,3-Glc); however, the activity for kojibiose (Glc-α-1,2-Glc), a terminal structure of Glc 3 Man 9 GlcNAc 2 , was 0.3% of that for nigerose. The enzyme also weakly hydrolyzes trehalose, maltose, and maltooligosaccharides, suggesting that the substrate specificity of E. coli YgjK is low (9). The catalytic residues of GH15 are identified as 2 glutamic acid residues, while in the case of GH37 and GH63, an aspartic acid residue and a glutamic acid residue function as the general acid and the general base, respectively, but the positions of the catalytic residues are highly conserved (8,9).…”

“…The enzyme also weakly hydrolyzes trehalose, maltose, and maltooligosaccharides, suggesting that the substrate specificity of E. coli YgjK is low (9). The catalytic residues of GH15 are identified as 2 glutamic acid residues, while in the case of GH37 and GH63, an aspartic acid residue and a glutamic acid residue function as the general acid and the general base, respectively, but the positions of the catalytic residues are highly conserved (8,9). Superimposition studies of GH37 (E. coli Tre37A) and GH63 (E. coli YgjK and T. thermophilus uncharacterized protein TTHA0978) show that the main chains of their catalytic (α/α) 6 barrel domains are overlain (Fig.…”

“…1D) (8), which hydrolyzes α-1,4-, α-1,6-, and α-1,1-glucosidic linkages, respectively, and Escherichia coli YgjK (Fig. 1E) (9), an enzyme that hydrolyzes the α-1,3-glucosidic linkage of nigerose. All these enzymes contain an α-helix-rich domain, designated as the (α/α)6 barrel, where the catalytic residues are located, and most of the enzymes have a β-sandwich domain at the N-terminus.…”

Function and Structure Studies of GH Family 31 and 97 α-Glycosidases

“…Recently, a tertiary structure of a homolog of the processing enzyme derived from E. coli (YgjK) was described. 13) The structure is composed of a -sandwich domain and a catalytic domain. The catalytic domain displays an one characterized enzyme, derived from Pyrococcus furiosus.…”