EzCatDB: D00462

DB codeD00462
RLCP classification1.13.200.966
CATH domainDomain 12.60.120.230Catalytic domain
Domain 22.60.120.230Catalytic domain
E.C.3.5.1.52
CSA1pgs

CATH domainRelated DB codes (homologues)
2.60.120.230M00214

Enzyme Name
Swiss-protKEGG

P21163
Protein namePeptide-N(4)-(N-acetyl-beta-D-glucosaminyl)asparagine amidase Fpeptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase
glycopeptide N-glycosidase
glycopeptidase
N-oligosaccharide glycopeptidase
N-glycanase
Jack-bean glycopeptidase
PNGase A
PNGase F
SynonymsPNGase F
EC 3.5.1.52
Glycopeptide N-glycosidase
N-glycanase


Swiss-prot:Accession NumberP21163
Entry namePNGF_ELIMR
ActivityHydrolysis of an N(4)-(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.
SubunitMonomer.
Subcellular location
Cofactor


SubstratesProductsintermediates
KEGG-idC04540C00001C01239C00012I00137
CompoundN4-(Acetyl-beta-D-glucosaminyl)asparagineH2ON-Acetyl-beta-D-glucosaminylaminePeptideAmino-diol-tetrahedral intermediate of N4-(Acetyl-beta-D-glucosaminyl)asparagine
Typeamino acids,amide group,carbohydrateH2Oamide group,amine group,carbohydratepeptide/protein
1pgsA01Unbound
UnboundUnboundUnbound
1pnfA01Unbound
Analogue:NDG-NAGUnboundUnbound
1pngA01Unbound
UnboundUnboundUnbound
1pgsA02Unbound
UnboundUnboundUnbound
1pnfA02Unbound
UnboundUnboundUnbound
1pngA02Unbound
UnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P21163 & literature [7]
pdbCatalytic residues
1pgsA01ASP  60
1pnfA01ASP  60
1pngA01ASP  60
1pgsA02GLU 206
1pnfA02GLU 206
1pngA02GLU 206

References for Catalytic Mechanism
ReferencesSectionsNo. of steps in catalysis
[7]p.29497
[11]Fig. 7, p.12958

references
[1]
PubMed ID2203781
JournalJ Biol Chem
Year1990
Volume265
Pages15606-10
AuthorsLemp D, Haselbeck A, Klebl F
TitleMolecular cloning and heterologous expression of N-glycosidase F from Flavobacterium meningosepticum.
[2]
PubMed ID2182634
JournalJ Biol Chem
Year1990
Volume265
Pages6961-6
AuthorsTarentino AL, Quinones G, Trumble A, Changchien LM, Duceman B, Maley F, Plummer TH Jr
TitleMolecular cloning and amino acid sequence of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase from flavobacterium meningosepticum.
[3]
PubMed ID1560183
JournalJ Biochem Biophys Methods
Year1992
Volume24
Pages71-9
AuthorsGosselin S, Martin BM, Murray GJ, Viswanatha T
TitleFlavobacterium meningosepticum peptide:N-glycosidase: influence of ionic strength on enzymatic activity.
[4]
CommentsX-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
Medline ID95001878
PubMed ID7918386
JournalBiochemistry
Year1994
Volume33
Pages11699-706
AuthorsKuhn P, Tarentino AL, Plummer TH Jr, Van Roey P
TitleCrystal structure of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F at 2.2-A resolution.
Related PDB1png
Related Swiss-protP21163
[5]
PubMed ID8057383
JournalJ Mol Biol
Year1994
Volume241
Pages622-3
AuthorsKuhn P, Tarentino AL, Plummer TH Jr, Van Roey P
TitleCrystallization and preliminary crystallographic analysis of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase PNGase F.
[6]
CommentsX-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
Medline ID95187708
PubMed ID7881905
JournalStructure
Year1994
Volume2
Pages1049-59
AuthorsNorris GE, Stillman TJ, Anderson BF, Baker EN
TitleThe three-dimensional structure of PNGase F, a glycosylasparaginase from Flavobacterium meningosepticum.
Related PDB1pgs
Related Swiss-protP21163
[7]
CommentsX-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS), AND MUTAGENESIS.
Medline ID96094350
PubMed ID7493989
JournalJ Biol Chem
Year1995
Volume270
Pages29493-7
AuthorsKuhn P, Guan C, Cui T, Tarentino AL, Plummer TH Jr, Van Roey P
TitleActive site and oligosaccharide recognition residues of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F.
Related PDB1pnf
Related Swiss-protP21163
[8]
PubMed ID11978727
JournalFASEB J
Year2002
Volume16
Pages635-41
AuthorsSuzuki T, Park H, Lennarz WJ
TitleCytoplasmic peptide:N-glycanase (PNGase) in eukaryotic cells: occurrence, primary structure, and potential functions.
[9]
PubMed ID11487565
JournalHum Mol Genet
Year2001
Volume10
Pages1627-30
AuthorsAnantharaman V, Koonin EV, Aravind L
TitlePeptide-N-glycanases and DNA repair proteins, Xp-C/Rad4, are, respectively, active and inactivated enzymes sharing a common transglutaminase fold.
[10]
PubMed ID11812789
JournalJ Biol Chem
Year2002
Volume277
Pages12953-9
AuthorsKatiyar S, Suzuki T, Balgobin BJ, Lennarz WJ
TitleSite-directed mutagenesis study of yeast peptide:N-glycanase. Insight into the reaction mechanism of deglycosylation.
[11]
PubMed ID15351714
JournalBiochem Biophys Res Commun
Year2004
Volume323
Pages149-55
AuthorsBiswas S, Katiyar S, Li G, Zhou X, Lennarz WJ, Schindelin H
TitleThe N-terminus of yeast peptide: N-glycanase interacts with the DNA repair protein Rad23.
[12]
PubMed ID14726951
JournalEMBO Rep
Year2004
Volume5
Pages201-6
AuthorsHirsch C, Misaghi S, Blom D, Pacold ME, Ploegh HL
TitleYeast N-glycanase distinguishes between native and non-native glycoproteins.

comments
This enzyme catalyzes hydrolysis of amide bond between N-acetyl-glucosamine and a sidechain of an asparagine residue in a peptide.
According to the literature [7], this enzyme has got two acidic residues (Asp60 & Glu206), which are interacting with each other, as catalytic residues. Whilst Asp60 seems to be directly involved in catalysis, Glu206 may act as a stabilizer for the reaction intermediate, or interact with the sidechain of the asparagine residue from the substrate peptide(see [7]). (These results suggest that this enzyme might have a similar mechanism to that of pepsin families.)
In contrast, all the eukaryotic counterpart enzymes contain a catalytic triad (Cys/His/Asp), suggesting that they have a similar mechanism to that of Cystein proteases, according to the literature [9] & [10].

createdupdated
2005-03-012012-06-29
Copyright: Nozomi Nagano, JST & CBRC-AIST
Funded by PRESTO/Japan Science and Technology Corporation (JST) (December 2001 - November 2004)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
Funded by Grant-in-Aid for Scientific Research (B)/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2010)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)

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