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Information on EC 3.5.1.52 - peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase and Organism(s) Saccharomyces cerevisiae and UniProt Accession Q02890
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3.5.1.52 peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidaseIUBMB Comments
Does not act on (GlcNAc)Asn, because it requires the presence of more than two amino-acid residues in the substrate [cf. EC 3.5.1.26, N4-(beta-N-acetylglucosaminyl)-L-asparaginase]. The plant enzyme was previously erroneously listed as EC 3.2.2.18.
Specify your search results
Word Map
- 3.5.1.52
-
deglycosylation
- n-glycans
- lectin
- glycopeptides
-
sialic
-
endoglycosidase
- mannose
- neuraminidase
-
o-linked
- tunicamycin
-
sialylated
- n-acetylglucosamine
-
asparagine-linked
- fucose
- glcnac
-
concanavalin
-
high-mannose
- agglutinin
-
complex-type
-
fucosylated
- sialidase
-
glycoforms
-
endo-beta-n-acetylglucosaminidase
-
biantennary
-
glycomics
-
asn-linked
-
high-mannose-type
-
glycoproteomic
- n-acetyllactosamine
- almond
-
tetraantennary
- 2-aminopyridine
- meningosepticum
- n-glycoproteins
- endo-beta-galactosidase
- fetuin
- analysis
- keratanase
-
permethylated
-
3hglucosamine
-
hybrid-type
-
mannose-type
-
oligomannosidic
- synthesis
-
hydrazinolysis
- man9glcnac2
-
trifluoromethanesulfonic
-
pyridylaminated
-
high-ph
-
oligomannose
-
retrotranslocation
- neu5ac
The taxonomic range for the selected organisms is: Saccharomyces cerevisiae
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea
Reaction Schemes
Synonyms
n-glycanase, pngase f, n-glycosidase f, pngase, peptide n-glycosidase f, ngly1, peptide-n-glycosidase f, glycopeptidase, peptide:n-glycosidase, peptide:n-glycanase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
acid PNGase M
-
-
-
-
glycopeptidase
-
-
-
-
glycopeptide N-glycosidase
-
-
-
-
jackbean glycopeptidase
-
-
-
-
L-929 PNGase
-
-
-
-
N-glycanase
-
-
-
-
N-oligosaccharide glycopeptidase
-
-
-
-
neutral PNGase M
-
-
-
-
peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F
-
-
-
-
peptide:N-glycanase
-
-
PNGase A
-
-
-
-
PNGase At
-
-
-
-
PNGase F
PNGase J
-
-
-
-
PNGase Os
-
-
-
-
PNGase Se
-
-
-
-
PNGase F
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Hydrolysis of an N4-(acetyl-beta-D-glucosaminyl)asparagine residue in which the glucosamine residue may be further glycosylated, to yield a (substituted) N-acetyl-beta-D-glucosaminylamine and a peptide containing an aspartate residue
Hydrolysis of an N4-(acetyl-beta-D-glucosaminyl)asparagine residue in which the glucosamine residue may be further glycosylated, to yield a (substituted) N-acetyl-beta-D-glucosaminylamine and a peptide containing an aspartate residue
mechanism and catalytic center
-
Hydrolysis of an N4-(acetyl-beta-D-glucosaminyl)asparagine residue in which the glucosamine residue may be further glycosylated, to yield a (substituted) N-acetyl-beta-D-glucosaminylamine and a peptide containing an aspartate residue
the catalytic triad is formed by Cys191, His218, and Asp235
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hydrolysis of carboxylic acid amide
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
N-linked-glycopeptide-(N-acetyl-beta-D-glucosaminyl)-L-asparagine amidohydrolase
Does not act on (GlcNAc)Asn, because it requires the presence of more than two amino-acid residues in the substrate [cf. EC 3.5.1.26, N4-(beta-N-acetylglucosaminyl)-L-asparaginase]. The plant enzyme was previously erroneously listed as EC 3.2.2.18.
CAS REGISTRY NUMBER
COMMENTARY
83534-39-8
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
Leu-Asn(GlcNAc5Man3Gal3)-Asp-Ser-Arg + H2O
?
fetuin-derived asialoglycopeptide I, 14C, substrate activity assay
-
-
?
alpha1-antitrypsin Pi Z + H2O
deglycosylated alpha1-antitrypsin Pi Z
-
-
-
?
ovalbumin + H2O
?
-
deglycosylation of the heat-denatured protein
-
-
?
ribonuclease B + H2O
?
-
When ribonuclease B is denatured at 60-65ºC or by 40-60 mM dithiothreitol, its deglycosylation by Png1p is most prominent
-
-
?
ricin A + H2O
?
-
deglycosylation of ricin A, the enzyme acts in complex with protein Rad23, interaction and complex formation analysis, overview
-
-
?
yeast carboxypeptidase + H2O
?
-
deglycosylation of heat-denatured protein
-
-
?
additional information
?
-
catalyses the de-glycosylation of unfolded glycoproteins
-
-
?
additional information
?
-
-
catalyses the de-glycosylation of unfolded glycoproteins
-
-
?
additional information
?
-
protein-protein interaction involving the cytoplasmic peptide:N-glycanase with DNA repair-related protein Rad23
-
-
?
additional information
?
-
-
protein-protein interaction involving the cytoplasmic peptide:N-glycanase with DNA repair-related protein Rad23
-
-
?
additional information
?
-
-
ability of enzyme to distinguish between native and misfolded substrates
-
?
additional information
?
-
-
overview on in vivo glycoprotein substrates
-
?
additional information
?
-
-
involved in proteasomal degradation of misfolded glycoproteins
-
?
additional information
?
-
-
the cytosolic enzyme deglycosylates misfolded glycoproteins prior to the endoplasmic reticulum-associated protein degradation
-
-
?
additional information
?
-
-
the enzyme is responsible for deglycosylation of N-linked glycoproteins dislocated from endoplasmic reticulum to cytosol
-
-
?
additional information
?
-
-
the deglycosylating enzyme catalyzes the hydrolysis of the beta-aspartylglycosylamine bond of asparagine-linked glycopeptides and glycoproteins, the misfolding or denaturation of glycoproteins is a prerequisite for enzyme activity
-
-
?
additional information
?
-
-
the enzyme hydrolyzes the beta-aspartylglycosylamine bond of asparagine-linked glycopeptides and glycoproteins, releasing an intact oligosaccharide and generating an aspartic acid residue at the cleavage site, the N-terminus of the enzyme interacts with the DNA repair protein Rad23 detected by gel filtration and surface plasmon resonance, quantitation of complex formation
-
-
?
additional information
?
-
-
peptide:N-glycanase catalyzes the detachment of N-linked glycan chains from glycopeptides or glycoproteins by hydrolyzing the beta-aspartylglucosaminyl bond. PNGase can not deglycosylate correctly folded native glycoproteins, but catalyzes the deglycosylation of misfolded glycoproteins. The complex formed between peptide:N-glycanase and Rad23p exhibits enhanced deglycosylation activity
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
additional information
?
-
catalyses the de-glycosylation of unfolded glycoproteins
-
-
?
additional information
?
-
-
catalyses the de-glycosylation of unfolded glycoproteins
-
-
?
additional information
?
-
protein-protein interaction involving the cytoplasmic peptide:N-glycanase with DNA repair-related protein Rad23
-
-
?
additional information
?
-
-
protein-protein interaction involving the cytoplasmic peptide:N-glycanase with DNA repair-related protein Rad23
-
-
?
additional information
?
-
-
involved in proteasomal degradation of misfolded glycoproteins
-
?
additional information
?
-
-
the cytosolic enzyme deglycosylates misfolded glycoproteins prior to the endoplasmic reticulum-associated protein degradation
-
-
?
additional information
?
-
-
the enzyme is responsible for deglycosylation of N-linked glycoproteins dislocated from endoplasmic reticulum to cytosol
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
benzyloxycarbonyl-Val-Ala-Asp-fluoromethylketone
-
covalently bind to the active site Cys191 of recombinant yeast peptide N-glycanase
carbobenzyloxy-Val-Ala-Asp-alpha-fluoromethylketone
-
i.e. Z-VAD-fmk, a broad-spectrum caspase inhibitor, IC50: 0.05 mM, binds covalently to the active site of the yeast enzyme, no restoration of enzyme activity by dialysis
Man9GlcNAc2-iodoacetoamide
-
strong inhibitor, irreversibly inhibits that catalytic Cys in a highly specific manner
Z-VAD-fmk
-
i.e. carbobenzyloxy-Val-Ala-Asp-alpha-fluoromethylketone, a broad-spectrum caspase inhibitor, potent inhibition, binding structure determination and analysis with wild-type and mutant C191A enzyme, the inhibitor binds covalently to the catalytic residue Cys191, but not to the catalytic His218
additional information
-
the enzyme is preferably inhibited by aspartate-based inhibitors
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.05
carbobenzyloxy-Val-Ala-Asp-alpha-fluoromethylketone
Saccharomyces cerevisiae
-
i.e. Z-VAD-fmk, a broad-spectrum caspase inhibitor, IC50: 0.05 mM, binds covalently to the active site of the yeast enzyme, no restoration of enzyme activity by dialysis
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7
-
the optimum deglycosylation pH of the Png1p-Rad23p complex is pH 7.0
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5 - 10
-
pH 5: about 50% of maximal activity, pH 10.0: about 70% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30
30
-
the optimum deglycosylation temperature of the Png1p-Rad23p complex is 30°C
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
20 - 37
-
20°C: about 60% of maximal activity, 37°C: about 55% of maximal activity
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
in yeast cells, the absence of cytoplasmic PNGase (Png1) results in significant reduction of the levels of free oligosaccharidesfound in the cytosol, suggesting that the majority, if not all, of the free oligosaccharidesin yeast are generated from misfolded glycoproteins in a PNGase-dependent manner. Phenotypes/pathological conditions caused by mutations in gene orthologues of cytoplasmic PNGase are defect in ERAD, but no growth/viability defects
physiological function
-
the complex formed between peptide:N-glycanase and Rad23p exhibits enhanced deglycosylation activity, which suggests an important role for this enzyme in the misfolded glycoprotein degradation pathway in vivo
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
-
enzyme-Rad23 interaction and complex formation analysis, the UBA domain of Rad23 is required, rad mutant does not interact with the enzyme, overview
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
the crystal structure of PNGase in complex with N,N'-diacetylchitobiose is described, refined at 3.4 A
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Q239A
mutation near the nonreducing end of the chitobiose, possible mannose binding site
Q243A
mutation near the nonreducing end of the chitobiose, possible mannose binding site
C191A
D235A
H218A
H218Y
-
site-directed mutagenesis, the mutant is inactive in protein glycosylation, but interacts with protein Rad23
additional information
C191A
-
site-directed mutagenesis, inactive mutant, inhibitor Z-VAD-fmk does not bind to the mutant enzyme
C191A
-
mutant enzyme does not bind to the inhibitor Man9GlcNAc2-iodoacetoamide
additional information
-
enzyme deletion strain, formation of free oligosaccharides is reduced by 70-80%
additional information
-
site-directed mutagenesis of not conserved amino acids
additional information
-
deletion of the N-terminal H1 helix (Png1p-DH1) enhances the deglycosylation activity of peptide:N-glycanase towards denatured glycoproteins
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25
-
stable up to 24 h, unstable at temperatures above 30°C after 1-3 h
37 - 45
-
Png1p is inactive at 37°C. In contrast, the Png1p-Rad23p complex still possesses enzymatic activity at 45°C
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant wild-type and mutant Png1 from Escherichia coli strain BL21(DE3)
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
into the vector pET28a for expression in Escherichia coli BL21DE3 Codon Plus RIL cells
co-expression of His6-tagged full-length enzyme or truncated versions with full-length Rad23 Escherichia coli strain BL21(DE3)
-
expression of His- or FLAG-tagged wild-type and mutant enzymes, co-expression with Rad23
-
gene png1, expression of wild-type and mutant Png1 in Escherichia coli strain BL21(DE3)
-
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Suzuki, T.; Park, H.; Kitajima, K.; Lennarz, W.J.
Peptides glycosylated in the endoplasmatic reticulum of yeast are subsequently deglycosylated by a soluble peptide:N-glycanase activity
J. Biol. Chem.
273
21526-21530
1998
Saccharomyces cerevisiae
Chantret, I.; Frenoy, J.P.; Moore, S.E.H.
Free-oligosaccharide control in the yeast Saccharomyces cerevisiae: roles for peptide:N-glycanase (Png1p) and vacuolar mannosidase (Ams1p)
Biochem. J.
373
901-908
2003
Saccharomyces cerevisiae
Hirsch, C.; Misaghi, S.; Blom, D.; Pacold, M.E.; Ploegh, H.L.
Yeast N-glycanase distinguishes between native and non-native glycoproteins
EMBO Rep.
5
201-206
2004
Saccharomyces cerevisiae
Suzuki, T.; Park, H.; Lennarz, W.J.
Cytoplasmic peptide:N-glycanase (PNGase) in eukaryotic cells: occurrence, primary structure, and potential functions
FASEB J.
16
635-641
2002
Saccharomyces cerevisiae
Katiyar, S.; Suzuki, T.; Balgobin, B.J.; Lennarz, W.J.
Site-directed mutagenesis study of yeast peptide: N-glycanase. Insight into the reaction mechanism of deglycosylation
J. Biol. Chem.
277
12953-12959
2002
Saccharomyces cerevisiae
Biswas, S.; Katiyar, S.; Li, G.; Zhou, X.; Lennarz, W.J.; Schindelin, H.
The N-terminus of yeast peptide: N-glycanase interacts with the DNA repair protein Rad23
Biochem. Biophys. Res. Commun.
323
149-155
2004
Saccharomyces cerevisiae
MIsaghi, S.; Korbel, G.A.; Kessler, B.; Spooner, E.; Ploegh, H.L.
Z-VAD-fmk inhibits peptide:N-glycanase and may result in ER stress
Cell Death Differ.
13
163-165
2006
Saccharomyces cerevisiae
Misaghi, S.; Pacold, M.; Blom, D.; Ploegh, H.L.; Korbel, G.A.
Using a small molecule inhibitor of peptide:N-glycanaseto probe its role in glycoprotein turnover
Chem. Biol.
11
1677-1687
2004
Saccharomyces cerevisiae, Homo sapiens, Mus musculus
Joshi, S.; Katiyar, S.; Lennarz, W.J.
Misfolding of glycoproteins is a prerequisite for peptide; N-glycanase mediated deglycosylation
FEBS Lett.
579
823-826
2005
Saccharomyces cerevisiae
Kim, I.; Ahn, J.; Liu, C.; Tanabe, K.; Apocadaca, J.; Suzuki, T.; Rao, H.
The Png1-Rad23 complex regulates glycoprotein turnover
J. Cell Biol.
172
211-219
2006
Saccharomyces cerevisiae
Wang, S.; Wang, P.G.; Qi, Q.
Influence of substrate conformation on the deglycosylation of ribonuclease B by recombinant yeast peptide:N-glycanase
Acta Biochim. Biophys. Sin. (Shanghai)
39
8-14
2007
Saccharomyces cerevisiae
Hagihara, S.; Miyazaki, A.; Matsuo, I.; Tatami, A.; Suzuki, T.; Ito, Y.
Fluorescently labeled inhibitor for profiling cytoplasmic peptide:N-glycanase
Glycobiology
17
1070-1076
2007
Saccharomyces cerevisiae
Suzuki, T.; Hara, I.; Nakano, M.; Zhao, G.; Lennarz, W.J.; Schindelin, H.; Taniguchi, N.; Totani, K.; Matsuo, I.; Ito, Y.
Site-specific labeling of cytoplasmic peptide:N-glycanase by N,N-diacetylchitobiose-related compounds
J. Biol. Chem.
281
22152-22160
2006
Saccharomyces cerevisiae
Witte, M.D.; Descals, C.V.; de Lavoir, S.V.; Florea, B.I.; van der Marel, G.A.; Overkleeft, H.S.
Bodipy-VAD-Fmk, a useful tool to study yeast peptide N-glycanase activity
Org. Biomol. Chem.
5
3690-3697
2007
Saccharomyces cerevisiae
Suzuki, T.
Cytoplasmic peptide:N-glycanase and catabolic pathway for free N-glycans in the cytosol
Semin. Cell Dev. Biol.
18
762-769
2007
Arabidopsis thaliana, Saccharomyces cerevisiae, Mus musculus
Zhao, G.; Li, G.; Zhou, X.; Matsuo, I.; Ito, Y.; Suzuki, T.; Lennarz, W.J.; Schindelin, H.
Structural and mutational studies on the importance of oligosaccharide binding for the activity of yeast PNGase
Glycobiology
19
118-125
2009
Saccharomyces cerevisiae (Q02890), Saccharomyces cerevisiae
Maerz, S.; Funakoshi, Y.; Negishi, Y.; Suzuki, T.; Seiler, S.
The Neurospora peptide:N-glycanase ortholog PNG1 is essential for cell polarity despite its lack of enzymatic activity
J. Biol. Chem.
285
2326-2332
2010
Saccharomyces cerevisiae, Neurospora crassa
Wang, S.; Xin, F.; Liu, X.; Wang, Y.; An, Z.; Qi, Q.; Wang, P.G.
N-terminal deletion of peptide:N-glycanase results in enhanced deglycosylation activity
PLoS ONE
4
e8335
2009
Saccharomyces cerevisiae, Elizabethkingia meningoseptica, Schizosaccharomyces pombe
Funakoshi, Y.; Negishi, Y.; Gergen, J.P.; Seino, J.; Ishii, K.; Lennarz, W.J.; Matsuo, I.; Ito, Y.; Taniguchi, N.; Suzuki, T.
Evidence for an essential deglycosylation-independent activity of PNGase in Drosophila melanogaster
PLoS ONE
5
e10545
2010
Saccharomyces cerevisiae, Drosophila melanogaster
Suzuki, T.
The cytoplasmic peptide N-glycanase (Ngly1) - basic science encounters a human genetic disorder
J. Biochem.
157
23-34
2015
Oryzias latipes, Neurospora crassa (D1MY48), Schizosaccharomyces pombe (O74739), Saccharomyces cerevisiae (Q02890), Saccharomyces cerevisiae, Dictyostelium discoideum (Q55FC8), Drosophila melanogaster (Q7KRR5), Homo sapiens (Q96IV0), Homo sapiens, Arabidopsis thaliana (Q9FGY9), Mus musculus (Q9JI78), Caenorhabditis elegans (Q9TW67), Schizosaccharomyces pombe ATCC 24843 (O74739), Schizosaccharomyces pombe 972 (O74739), Saccharomyces cerevisiae ATCC 204508 (Q02890)
EXTERNAL LINKS (specific for EC-Number 3.5.1.52)
Transporter Classification Database (TCDB): 3.A.16.1.5
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