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Hirayama H, Fujihira H, Suzuki T. Development of new NGLY1 assay systems - toward developing an early screening method for NGLY1 deficiency. Glycobiology 2024; 34:cwae067. [PMID: 39206713 PMCID: PMC11442003 DOI: 10.1093/glycob/cwae067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 08/19/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024] Open
Abstract
Cytosolic peptide: N-glycanase (PNGase/NGLY1 in mammals) is an amidase (EC:3.5.1.52) widely conserved in eukaryotes. It catalyzes the removal of N-glycans on glycoproteins, converting N-glycosylated Asn into Asp residues. This enzyme also plays a role in the quality control system for nascent glycoproteins. Since the identification of a patient with an autosomal recessive genetic disorder caused by NGLY1 gene dysfunction, known as NGLY1 deficiency or NGLY1 congenital disorder of deglycosylation (OMIM: 615273), in 2012, more than 100 cases have been reported worldwide. NGLY1 deficiency is characterized by a wide array of symptoms, such as global mental delay, intellectual disability, abnormal electroencephalography findings, seizure, movement disorder, hypolacrima or alacrima, and liver dysfunction. Unfortunately, no effective therapeutic treatments for this disease have been established. However, administration of adeno-associated virus 9 (AAV9) vector harboring human NGLY1 gene to an NGLY1-deficient rat model (Ngly1-/- rat) by intracerebroventricular injection was found to drastically improve motor function defects. This observation indicated that early therapeutic intervention could alleviate various symptoms originating from central nervous system dysfunction in this disease. Therefore, there is a keen interest in the development of facile diagnostic methods for NGLY1 deficiency. This review summarizes the history of assay development for PNGase/NGLY1 activity, as well as the recent progress in the development of novel plate-based assay systems for NGLY1, and also discusses future perspectives.
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Affiliation(s)
- Hiroto Hirayama
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), Riken, 2-1 Hirosawa, Wako Saitama 351-0198, Japan
| | - Haruhiko Fujihira
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), Riken, 2-1 Hirosawa, Wako Saitama 351-0198, Japan
| | - Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research (CPR), Riken, 2-1 Hirosawa, Wako Saitama 351-0198, Japan
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Hirayama H, Suzuki T. Assay for the peptide:N-glycanase/NGLY1 and disease-specific biomarkers for diagnosing NGLY1 deficiency. J Biochem 2021; 171:169-176. [PMID: 34791337 DOI: 10.1093/jb/mvab127] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 11/11/2021] [Indexed: 11/13/2022] Open
Abstract
Cytosolic peptide:N-glycanase (NGLY1 in mammals), a highly conserved enzyme in eukaryotes, catalyzes the deglycosylation of N-glycans that are attached to glycopeptide/glycoproteins. In 2012, an autosomal recessive disorder related to the NGLY1 gene, which was referred to as NGLY1 deficiency, was reported. Since then, more than 100 patients have been identified. Patients with this disease exhibit various symptoms, including various motor deficits and other neurological problems. Effective therapeutic treatments for this disease, however, have not been established. Most recently, it was demonstrated that the intracerebroventricular administration of an adeno-associated virus 9 vector expressing human NGLY1 during the weaning period allowed some motor functions to be recovered in Ngly1-/- rats. This observation led us to hypothesize that a therapeutic intervention for improving these motor deficits or other neurological symptoms found in the patients might be possible. To achieve this, it is critical to establish robust and facile methods for assaying NGLY1 activity in biological samples, for the early diagnosis and evaluation of the therapeutic efficacy for the treatment of NGLY1 deficiency. In this mini-review, we summarize progress made in the development of various assay methods for NGLY1 activity, as well as a recent progress in the identification of NGLY1 deficiency-specific biomarkers.
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Affiliation(s)
- Hiroto Hirayama
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Japan.,Takeda-CiRA Joint Program (T-CiRA), Kanagawa, Japan
| | - Tadashi Suzuki
- Glycometabolic Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, RIKEN, Japan.,Takeda-CiRA Joint Program (T-CiRA), Kanagawa, Japan
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Wang MM, Laborda P, Conway LP, Duan XC, Huang K, Liu L, Voglmeir J. An integrated 3D-printed platform for the automated isolation of N-glycans. Carbohydr Res 2016; 433:14-7. [DOI: 10.1016/j.carres.2016.06.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 06/22/2016] [Accepted: 06/23/2016] [Indexed: 12/13/2022]
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Hirayama H, Hosomi A, Suzuki T. Physiological and molecular functions of the cytosolic peptide:N-glycanase. Semin Cell Dev Biol 2015; 41:110-20. [DOI: 10.1016/j.semcdb.2014.11.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 11/25/2014] [Accepted: 11/26/2014] [Indexed: 01/04/2023]
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5
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Léonard R, Strasser R, Altmann F. Plant glycosidases acting on protein-linked oligosaccharides. PHYTOCHEMISTRY 2009; 70:318-24. [PMID: 19200565 DOI: 10.1016/j.phytochem.2009.01.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Accepted: 01/11/2009] [Indexed: 05/20/2023]
Abstract
Glycosidases have been used as invaluable tools in glycobiology research for decades, and their role in glycoprotein maturation has been amply studied. The molecular biological coverage of this large group of enzymes has only recently reached an appreciable level. In this review, we present an overview of plant glycosidases, whose DNA/protein sequence has been identified and for which recombinant enzymes have been characterized. The physiological role in the maturation of glycoproteins is discussed as well as the biotechnological prospects arising from knowing the enzymes responsible for the removal of terminal N-acetylglucosamine residues. The current knowledge on plant fucosidases and of the first bits of information on glycosidases acting on arabinogalactan proteins is presented.
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Affiliation(s)
- Renaud Léonard
- Department of Chemistry, University of Natural Resources and Applied Life Sciences (BOKU), 1190 Vienna, Austria.
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6
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Xia YQ, Risley JM. SYNTHESIS OFN4-(2-ACETAMIDO-2-DEOXY-β-D-GLUCOPYRANOSYL)-L-ASPARAGINE ANALOGUES.L-2-CHLORO-,L-2-BROMO-, ANDD,L-2-METHYLSUCCINAMIC ACID ANALOGUES. J Carbohydr Chem 2001. [DOI: 10.1081/car-100102542] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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7
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Sugars, Polysaccharides, and Glycoproteins. Biochemistry 2001. [DOI: 10.1016/b978-012492543-4/50007-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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8
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De Huang H, Risley JM. Synthesis of N4-(2-acetamido-2-deoxy-beta-D-glucopyranosyl)-L-asparagine analogues: succinamide, L-2-hydroxysuccinamide, and L-2-hydroxysuccinamic acid hydrazide analogues. Carbohydr Res 2000; 329:487-93. [PMID: 11128578 DOI: 10.1016/s0008-6215(00)00224-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The syntheses of three analogues of N4-(2-acetamido-2-deoxy-beta-D-glucopyranosyl)-L-asparagine are described. N-(2-Acetamido-2-deoxy-beta-D-glucopyranosyl)succinamide was synthesized by the reaction of pentafluorophenyl succinamate with 2-acetamido-2-deoxy-beta-D-glucopyranosylamine. 2-Acetamido-3,4,6-tri-O-acetyl-2-deoxy-beta-D-glucopyranosylamine was synthesized, and the complete assignment of the 1H NMR spectrum is given. Reaction of the protected beta-D-glycosylamine with L-malic acid chloralid in the presence of a coupling agent (EEDQ) gave N4-(2-acetamido-3,4,6-tri-O-acetyl-2-deoxy-beta-D-glucopyranosyl)-L-malamic acid chloralid that was deprotected two ways: (1) using ammonia, which gave N4-(2-acetamido-2-deoxy-beta-D-glucopyranosyl)-L-2-hydroxysuccinamide, and (2) using hydrazine, which gave N4-(2-acetamido-2-deoxy-1-D-glucopyranosyl)-L-2-hydroxysuccinamic acid hydrazide.
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Affiliation(s)
- H De Huang
- Department of Chemistry, University of North Carolina at Charlotte, 28223, USA
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9
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Kimura Y, Ohno A. A new peptide-N4-(acetyl-beta-glucosaminyl)asparagine amidase from soybean (Glycine max) seeds: purification and substrate specificity. Biosci Biotechnol Biochem 1998; 62:412-8. [PMID: 9532807 DOI: 10.1271/bbb.62.412] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We report here the isolation and characterization of a peptide-N4-(acetyl-beta-glucosaminyl) asparagine amidase (peptide: N-glycanase) from soybean (Glycine max) seeds. The enzyme was purified to homogeneity with 6.5% yield from defatted soybean meal extract by ion-exchange chromatography, gel filtration, hydroxyapatite chromatography, and hydrophobic chromatography. The purified enzyme, designated PNGase-GM, had the apparent molecular mass of 93 kDa by SDS-PAGE and 90 kDa by gel filtration, indicating this PNGase is a monomeric protein. The enzyme showed maximal activity at pH 4.5-5.0. PNGase-GM was capable of hydrolyzing the beta-aspartylglycosylamine linkage (GlcNAc beta 1-->Asn) of various glycopeptide substrates bearing high-mannose type, hybrid type, and xylose/fucose-containing plant complex type N-glycan units, while this amidase was far less active on the glycopeptides bearing sialylated animal complex-type glycans.
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Affiliation(s)
- Y Kimura
- Department of Bioresources Chemistry, Faculty of Agriculture, Okayama University, Japan
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Wang LX, Tang M, Suzuki T, Kitajima K, Inoue Y, Inoue S, Fan JQ, Lee YC. Combined Chemical and Enzymatic Synthesis of a C-Glycopeptide and Its Inhibitory Activity toward Glycoamidases. J Am Chem Soc 1997. [DOI: 10.1021/ja9712027] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lai-Xi Wang
- Contribution from the Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, and Department of Biophysics and Biochemistry, University of Tokyo, Tokyo 113, Japan
| | - Mei Tang
- Contribution from the Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, and Department of Biophysics and Biochemistry, University of Tokyo, Tokyo 113, Japan
| | - Tadashi Suzuki
- Contribution from the Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, and Department of Biophysics and Biochemistry, University of Tokyo, Tokyo 113, Japan
| | - Ken Kitajima
- Contribution from the Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, and Department of Biophysics and Biochemistry, University of Tokyo, Tokyo 113, Japan
| | - Yasuo Inoue
- Contribution from the Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, and Department of Biophysics and Biochemistry, University of Tokyo, Tokyo 113, Japan
| | - Sadako Inoue
- Contribution from the Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, and Department of Biophysics and Biochemistry, University of Tokyo, Tokyo 113, Japan
| | - Jian-Qiang Fan
- Contribution from the Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, and Department of Biophysics and Biochemistry, University of Tokyo, Tokyo 113, Japan
| | - Yuan C. Lee
- Contribution from the Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, and Department of Biophysics and Biochemistry, University of Tokyo, Tokyo 113, Japan
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Altmann F, Schweiszer S, Weber C. Kinetic comparison of peptide: N-glycosidases F and A reveals several differences in substrate specificity. Glycoconj J 1995; 12:84-93. [PMID: 7540902 DOI: 10.1007/bf00731873] [Citation(s) in RCA: 79] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The initial velocities of hydrolysis of nineteen glycopeptides by peptide: N-glycosidase F and A were determined. Substrates were prepared from bovine fetuin, hen ovalbumin, pineapple stem bromelain, bovine fibrin and taka-amylase. From these glycopeptides, several variants with regard to peptide and carbohydrate structure were prepared and derivatized with dabsyl chloride, dansyl chloride or activated resorufin. Tyrosine containing glycopeptides were also used without an additional chromophore. Enzymatic hydrolysis of glycopeptides was quantified by narrow bore, reversed phase HPLC with turnaround cycle times of down to 6 min, but usually 15 min. KM values ranging from 30 to 64 microM and from 4 to 36 microM were found for N-glycosidase F and A, respectively. Relative velocities of hydrolysis of the different substrates by each enzyme varied considerably. Little, if any, similarity of the performance of N-glycosidase F and A with the different substrates was observed. The minimal carbohydrate structure released by peptide: N-glycosidase F was a di-N-acetylchitobiose. N-glycosidase A could release even a single N-acetylglucosamine, albeit 3000 times slower than a di-N-acetylchitobiose or larger glycans. In general the structure of the intact glycan had little effect on activity, and with both enzymes the rate of hydrolysis appeared to be primarily governed by peptide structure and length. However, N-glycosidase F did not release glycans alpha 1,3-fucosylated at the asparagine linked N-acetylglucosamine irrespective of the presence of xylose in the substrate.
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Affiliation(s)
- F Altmann
- Institut für Chemie, Univesität fur Bodenkultur Wien, Austria
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Berger S, Menudier A, Julien R, Karamanos Y. Do de-N-glycosylation enzymes have an important role in plant cells? Biochimie 1995; 77:751-60. [PMID: 8789467 DOI: 10.1016/0300-9084(96)88193-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
In this review de-N-glycosylation was defined as the removal of the glycan(s) from a N-glycosylprotein, by means of enzymes acting on the di-N-acetylchitobiosyl part of the invariant pentasaccharide inner-core of N-glycosylproteins. Peptide-N4-(N-acetyl-beta-D-glucosaminyl) asparagine amidases (PNGase) and endo-N-acetyl-beta-D-glucosaminidases (ENGase) were both considered as de-N-glycosylation enzymes. A detailed description of the characterization and the function of plant PNGases and ENGases is presented, together with a brief presentation on the occurrence and the current knowledge on the function of microbial and animal enzymes. De-N-glycosylation of plant glycoproteins was proposed as a possible mechanism for the release of oligosaccharides displaying biological activities and the removal of N-glycans could also explain the regulation of protein activity. Each enzyme seems to have a specific function during germination and post-germinative development. All the arguments concur that de-N-glycosylation enzymes have an important role in plant cells and confirm that the N-glycosylation/de-N-glycosylation system should occur more commonly than presently recognized in living organisms.
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Affiliation(s)
- S Berger
- Institut de Biotechnologie, Université de Limoges, France
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Kuhn P, Tarentino AL, Plummer TH, Van Roey P. Crystal structure of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F at 2.2-A resolution. Biochemistry 1994; 33:11699-706. [PMID: 7918386 DOI: 10.1021/bi00205a005] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F (PNGase F) is an amidase that cleaves the beta-aspartylglucosylamine bond of asparagine-linked glycans. The 34.8-kDa (314 amino acids) enzyme has a very broad substrate specificity and is extensively used for studies of the structure and function of glycoproteins. Enzymatic activity of PNGase F requires recognition of both the peptide and the carbohydrate components of the substrate. Only limited information regarding the mechanism of action of the enzyme is available. The three-dimensional structure of PNGase F has been determined by X-ray crystallography at 2.2-A resolution. The protein folds into two domains comprising residues 1-137 and 143-314, respectively. Both domains have eight-stranded antiparallel beta-sandwich motifs that are very similar in geometry. Both sandwiches have parallel principal axes and lie side by side. The covalent link between the domains is located at the top end of the molecule. Extensive hydrogen-bonding contacts occur along the full length of the interface between the two domains. Three different areas, all at the interface between the two domains, have been identified as possible locations for the active site of the enzyme. These include a hydrophobic bowl of about 20 A in diameter on one surface of the molecule, a long polar cleft on the opposite side, and a cleft at the bottom, which is lined with large aromatic residues including eight tryptophans.
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Affiliation(s)
- P Kuhn
- Wadsworth Center, New York State Department of Health, Albany 12201-0509
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Gosselin S, Martin BM, Murray GJ, Viswanatha T. Flavobacterium meningosepticum peptide:N-glycosidase: influence of ionic strength on enzymatic activity. JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS 1992; 24:71-9. [PMID: 1560183 DOI: 10.1016/0165-022x(92)90048-f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Flavobacterium meningosepticum peptide:N-glycosidase-mediated deglycosylation of N-linked glycan strands of glycoproteins has been found to be strongly influenced by the ionic strength of the assay medium. By use of a modification of a previously published assay procedure for quantitative analysis of glycan release we have been able to improve reproducibility and thus to compare the extent of deglycosylation achieved under a variety of conditions of ionic strength. We have observed that enzyme activity is adversely affected by high ionic strength buffers such as those recommended for deglycosylation of various glycoproteins and recommend the use of low ionic strength buffers for routine use.
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Affiliation(s)
- S Gosselin
- Guelph-Waterloo Centre for Graduate Work in Chemistry, University of Waterloo, Ontario, Canada
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15
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Tretter V, Altmann F, März L. Peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase F cannot release glycans with fucose attached alpha 1----3 to the asparagine-linked N-acetylglucosamine residue. EUROPEAN JOURNAL OF BIOCHEMISTRY 1991; 199:647-52. [PMID: 1868849 DOI: 10.1111/j.1432-1033.1991.tb16166.x] [Citation(s) in RCA: 338] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The ability of peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase F (PNGase F) from Flavobacterium meningosepticum and PNGase A from sweet almonds to deglycosylate N-glycopeptides and N-glycoproteins from plants was compared. Bromelain glycopeptide and horseradish peroxidase-C glycoprotein, which contain xylose linked beta 1----2 to beta-mannose and fucose linked alpha 1----3 to the innermost N-acetylglucosamine, were used as substrates. In contrast to PNGase A, the enzyme from F. meningosepticum did not act upon these substrates even at concentrations 100-fold higher than required for complete deglycosylation of commonly used standard substrates. After removal of alpha 1----3-linked fucose from the plant glycopeptide and glycoprotein by mild acid hydrolysis, they were readily degraded by PNGase F at moderate enzyme concentrations. Hence we conclude that alpha 1----3 fucosylation of the inner N-acetylglucosamine impedes the enzymatic action of PNGase F. Knowledge of this limitation of the deglycosylation potential of PNGase F may turn it from a pitfall into a useful experimental tool.
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Affiliation(s)
- V Tretter
- Institut für Chemie der Universität für Bodenkultur Wien, Austria
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16
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Bovine glomerular basement membrane. Location and structure of the asparagine-linked oligosaccharide units and their potential role in the assembly of the 7 S collagen IV tetramer. J Biol Chem 1991. [DOI: 10.1016/s0021-9258(18)52290-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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17
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Altmann F, Kubelka V, Staudacher E, Uhl K, März L. Characterization of the isoforms of phospholipase A2 from honeybee venom. ACTA ACUST UNITED AC 1991. [DOI: 10.1016/0020-1790(91)90099-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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18
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Tarentino AL, Quinones G, Trumble A, Changchien LM, Duceman B, Maley F, Plummer TH. Molecular cloning and amino acid sequence of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase from flavobacterium meningosepticum. J Biol Chem 1990. [DOI: 10.1016/s0021-9258(19)39244-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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19
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A general strategy for the isolation of carbohydrate chains fromN-,O-glycoproteins and its application to human chorionic gonadotrophin. Glycoconj J 1987. [DOI: 10.1007/bf01049451] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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