DB code: D00462

RLCP classification 1.13.200.966 : Hydrolysis
CATH domain 2.60.120.230 : Jelly Rolls Catalytic domain
2.60.120.230 : Jelly Rolls Catalytic domain
E.C. 3.5.1.52
CSA 1pgs
M-CSA 1pgs
MACiE

CATH domain Related DB codes (homologues)
2.60.120.230 : Jelly Rolls M00214

Uniprot Enzyme Name
UniprotKB Protein name Synonyms Pfam
P21163 Peptide-N(4)-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F
PNGase F
EC 3.5.1.52
Glycopeptide N-glycosidase
N-glycanase
PF09113 (N-glycanase_C)
PF09112 (N-glycanase_N)
[Graphical View]

KEGG enzyme name
peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase
glycopeptide N-glycosidase
glycopeptidase
N-oligosaccharide glycopeptidase
N-glycanase
Jack-bean glycopeptidase
PNGase A
PNGase F

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P21163 PNGF_ELIMR Hydrolysis 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. Monomer.

KEGG Pathways
Map code Pathways E.C.

Compound table
Substrates Products Intermediates
KEGG-id C04540 C00001 C01239 C00012 I00137
E.C.
Compound N4-(Acetyl-beta-D-glucosaminyl)asparagine H2O N-Acetyl-beta-D-glucosaminylamine Peptide Amino-diol-tetrahedral intermediate of N4-(Acetyl-beta-D-glucosaminyl)asparagine
Type amino acids,amide group,carbohydrate H2O amide group,amine group,carbohydrate peptide/protein
ChEBI 17261
58080
15377
15947
PubChem 123826
25201322
22247451
962
439454
1pgsA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1pnfA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Analogue:NDG-NAG Unbound Unbound
1pngA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1pgsA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1pnfA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound
1pngA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P21163 & literature [7]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1pgsA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 60
1pnfA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 60
1pngA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ASP 60
1pgsA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 206
1pnfA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 206
1pngA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 206

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[7]
p.29497
[11]
Fig. 7, p.12958

References
[1]
Resource
Comments
Medline ID
PubMed ID 2203781
Journal J Biol Chem
Year 1990
Volume 265
Pages 15606-10
Authors Lemp D, Haselbeck A, Klebl F
Title Molecular cloning and heterologous expression of N-glycosidase F from Flavobacterium meningosepticum.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 2182634
Journal J Biol Chem
Year 1990
Volume 265
Pages 6961-6
Authors Tarentino AL, Quinones G, Trumble A, Changchien LM, Duceman B, Maley F, Plummer TH Jr
Title Molecular cloning and amino acid sequence of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase from flavobacterium meningosepticum.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 1560183
Journal J Biochem Biophys Methods
Year 1992
Volume 24
Pages 71-9
Authors Gosselin S, Martin BM, Murray GJ, Viswanatha T
Title Flavobacterium meningosepticum peptide:N-glycosidase: influence of ionic strength on enzymatic activity.
Related PDB
Related UniProtKB
[4]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
Medline ID 95001878
PubMed ID 7918386
Journal Biochemistry
Year 1994
Volume 33
Pages 11699-706
Authors Kuhn P, Tarentino AL, Plummer TH Jr, Van Roey P
Title Crystal structure of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F at 2.2-A resolution.
Related PDB 1png
Related UniProtKB P21163
[5]
Resource
Comments
Medline ID
PubMed ID 8057383
Journal J Mol Biol
Year 1994
Volume 241
Pages 622-3
Authors Kuhn P, Tarentino AL, Plummer TH Jr, Van Roey P
Title Crystallization and preliminary crystallographic analysis of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase PNGase F.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
Medline ID 95187708
PubMed ID 7881905
Journal Structure
Year 1994
Volume 2
Pages 1049-59
Authors Norris GE, Stillman TJ, Anderson BF, Baker EN
Title The three-dimensional structure of PNGase F, a glycosylasparaginase from Flavobacterium meningosepticum.
Related PDB 1pgs
Related UniProtKB P21163
[7]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS), AND MUTAGENESIS.
Medline ID 96094350
PubMed ID 7493989
Journal J Biol Chem
Year 1995
Volume 270
Pages 29493-7
Authors Kuhn P, Guan C, Cui T, Tarentino AL, Plummer TH Jr, Van Roey P
Title Active site and oligosaccharide recognition residues of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F.
Related PDB 1pnf
Related UniProtKB P21163
[8]
Resource
Comments
Medline ID
PubMed ID 11978727
Journal FASEB J
Year 2002
Volume 16
Pages 635-41
Authors Suzuki T, Park H, Lennarz WJ
Title Cytoplasmic peptide:N-glycanase (PNGase) in eukaryotic cells: occurrence, primary structure, and potential functions.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 11487565
Journal Hum Mol Genet
Year 2001
Volume 10
Pages 1627-30
Authors Anantharaman V, Koonin EV, Aravind L
Title Peptide-N-glycanases and DNA repair proteins, Xp-C/Rad4, are, respectively, active and inactivated enzymes sharing a common transglutaminase fold.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 11812789
Journal J Biol Chem
Year 2002
Volume 277
Pages 12953-9
Authors Katiyar S, Suzuki T, Balgobin BJ, Lennarz WJ
Title Site-directed mutagenesis study of yeast peptide:N-glycanase. Insight into the reaction mechanism of deglycosylation.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 15351714
Journal Biochem Biophys Res Commun
Year 2004
Volume 323
Pages 149-55
Authors Biswas S, Katiyar S, Li G, Zhou X, Lennarz WJ, Schindelin H
Title The N-terminus of yeast peptide: N-glycanase interacts with the DNA repair protein Rad23.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 14726951
Journal EMBO Rep
Year 2004
Volume 5
Pages 201-6
Authors Hirsch C, Misaghi S, Blom D, Pacold ME, Ploegh HL
Title Yeast N-glycanase distinguishes between native and non-native glycoproteins.
Related PDB
Related UniProtKB

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].

Created Updated
2005-03-01 2012-06-29