title: The structural basis of the difference in sensitivity for PNGase F in the de-N-glycosylation of the native bovine pancreatic ribonucleases B and BS.
abstract: In glycoanalysis protocols, N-glycans from glycoproteins are most frequently released with peptide- N (4)-( N-acetyl-beta-glucosaminyl)asparagine amidase F (PNGase F). As the enzyme is an amidase, it cleaves the NH-CO linkage between the Asn side chain and the Asn-bound GlcNAc residue. Usually, the enzyme has a low activity, or is not active at all, on native glycoproteins. A typical example is native bovine pancreatic ribonuclease B (RNase B) with oligomannose-type N-glycans at Asn-34. However, native RNase BS, generated by subtilisin digestion of native RNase B, which comprises amino acid residues 21-124 of RNase B, is sensitive to PNGase F digestion. The same holds for carboxymethylated RNase B (RNase B (cm)). In this study, NMR spectroscopy and molecular modeling have been used to explain the differences in PNGase F activity for native RNase B, native RNase BS, and RNase B (cm). NMR analysis combined with literature data clearly indicated that the N-glycan at Asn-34 is more mobile in RNase BS than in RNase B. MD simulations showed that the region around Asn-34 in RNase B is not very flexible, whereby the alpha-helix of the amino acid residues 1-20 has a stabilizing effect. In RNase BS, the alpha-helix formed by amino acid residues 23-32 is significantly more flexible. Using these data, the possibilities for complex formation of both RNase B and RNase BS with PNGase F were studied, and a model for the RNase BS-PNGase F complex is proposed.
authors.affiliation: Bijvoet Center, Department of Bio-Organic Chemistry, Utrecht University, Padualaan 8, NL-3584 CH Utrecht, The Netherlands.
authors.forename: Véronique
authors.initials: V
authors.lastname: Blanchard
authors.forename: Martin
authors.initials: M
authors.lastname: Frank
authors.forename: Bas R
authors.initials: BR
authors.lastname: Leeflang
authors.forename: Rolf
authors.initials: R
authors.lastname: Boelens
authors.forename: Johannis P
authors.initials: JP
authors.lastname: Kamerling
mesh_terms: D000818:Animals; D002240:Carbohydrate Sequence; D002417:Cattle; D003198:Computer Simulation; D006031:Glycosylation; D007527:Isoenzymes / Q000737:chemistry / Q000378:metabolism; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010179:Pancreas / Q000201:enzymology*; D043524:Peptide-N4-(N-acetyl-beta-glucosaminyl) Asparagine Amidase / Q000737:chemistry* / Q000378:metabolism*; D012260:Ribonucleases / Q000737:chemistry* / Q000378:metabolism*; D012997:Solvents; D013816:Thermodynamics
chemical_list: D007527:Isoenzymes; D012997:Solvents; D012260:Ribonucleases; C029600:ribonuclease B; D043524:Peptide-N4-(N-acetyl-beta-glucosaminyl) Asparagine Amidase