Removal of glycan groups from proteins via enzymatic methods is preferable to chemical removal because it is gentler and can provide complete sugar removal with no protein degradation.

Endoglycosidases cleave entire glycan groups from glycoproteins. The most commonly used endoglycosidase, Peptide-N-Glycosidase F (PNGase F) (NEB #P0704, NEB #P0708, NEB #P0706, NEB #P0710), is actually an amidase, which catalyzes the deglycosylation of most N-linked glycoproteins. The enzyme catalyzes the cleavage between the innermost N-Acetylglucosamine (GlcNAc) of the chitobiose core and the amine group of the asparagine residue (1).

There is a variety of endoglycosidases that are active on N-linked glycans. They all have identical cleavage sites between the two GlcNAc residues of the chitobiose core, but they recognize and cleave different types of N-linked glycans. Endoglycosidase H (Endo H) (NEB #P0702, NEB #P0703) cleaves within the chitobiose core of high mannose and some hybrid oligosaccharides from N-linked glycoproteins (1). Endoglycosidase S (Endo S) (NEB #P0741) is highly specific for removing N-linked glycans from the heavy chain of native IgG (2). While Endoglycosidase D (Endo D) (NEB #P0742) cleaves paucimannose N-linked glycans(3).

There are fewer endoglycosidases also called α-N-Acetylgalactosaminidases active on O-linked glycans. The majority of O-glycosidases found to date are active only on a disaccharide Galβ1,3GalNAcα-O-Ser/Thr requiring the removal of Sialic acid and any other attached sugar residues before the enzyme can catalyze the removal of this Core 1 disaccharide from the glycoprotein. However there is one enzyme with a slightly broader O-Glycosidase specificity (NEB #P0733, NEB #E0540), and it is able to catalyze the removal of Core 1 (Galβ1,3GalNAc) or Core 3 (GlcNAcβ1,3GalNAc) O-linked disaccharides from glycoproteins (4).


  1. Maley, F. et al.  (1989) Anal. Biochem., 180, 195-204.
    PMID: 2510544
  2. Collin, M. and Olsén, A. (2001). The EMBO Journal. 20, 3046-3055. PMID: 11406581
  3. Mizuochi, T. et al. (1984) J. Biochem. 95, 1209-1213.
    PMID: 6430882
  4. Koutsioulis, D., Landry, D. and Guthrie, E.P.  (2008) Glycobiology, 18, 799-805. PMID: 18635885
  1. Identification and Characterization of Protein Glycosylation P6039S

    Here we illustrate the use of glycosidases for the analysis of a model glycoprotein: recombinant human chorionic gonadotropin beta (hCGβ), which carries both N-glycans and O-glycans in this video. The technique requires only simple instrumentation and typical consumables, and it can be readily adapted to the analysis of multiple glycoprotein samples.

  2. Elucidating the Complexity of Heparin Oligosaccharide Analysis

    Learn more about the structural elucidation of complex and diverse heparin oligosaccharides using Bacteroides Heparinase I, II and III in combination with downstream mass spec analysis.