DB code: D00462

RLCP classification	1.13.200.966 : Hydrolysis
CATH domain	2.60.120.230 : Jelly Rolls	Catalytic domain
CATH 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 17261 58080	15377 15377	15947 15947
PubChem	123826 25201322 123826 25201322	22247451 962 22247451 962	439454 439454

1pgsA01	Unbound		Unbound	Unbound	Unbound
1pnfA01	Unbound		Analogue:NDG-NAG	Unbound	Unbound
1pngA01	Unbound		Unbound	Unbound	Unbound
1pgsA02	Unbound		Unbound	Unbound	Unbound
1pnfA02	Unbound		Unbound	Unbound	Unbound
1pngA02	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	ASP 60
1pnfA01	ASP 60
1pngA01	ASP 60
1pgsA02	GLU 206
1pnfA02	GLU 206
1pngA02	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].

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