Peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase
Peptide aspartylglucosaminidase (PNGase) removes asparagine linked oligosaccharide chains from intact proteins.
Reference Protein and Structure
- Sequence
-
P21163
(3.5.1.52)
(Sequence Homologues)
(PDB Homologues)
- Biological species
-
Elizabethkingia miricola (Bacteria)
- PDB
-
1pgs
- THE THREE-DIMENSIONAL STRUCTURE OF PNGASE F, A GLYCOSYLASPARAGINASE FROM FLAVOBACTERIUM MENINGOSEPTICUM
(1.8 Å)
- Catalytic CATH Domains
-
2.60.120.230
(see all for 1pgs)
Enzyme Reaction (EC:3.5.1.52)
+
→
+
+
Alternative enzyme names: N-glycanase, N-oligosaccharide glycopeptidase, Jack-bean glycopeptidase, PNGase A, PNGase F, Glycopeptidase, Glycopeptide N-glycosidase,
Enzyme Mechanism
Introduction
Very little information regarding the mechanism of action of the enzyme was available when the structures were determined (late 1990s). The mechanism is proposed to proceed in a similar manner to other peptidases in which a nucleophilic residue (thought to be Asp in this case) initiates a nucleophilic addition to the carbonyl carbon of the substrate peptide bond, eliminating the amine product. A general acid/base activates water, which then cleaves the carboxylic acid product from the enzyme.
Catalytic Residues Roles
| UniProt | PDB* (1pgs) | ||
| Glu158 | Glu118A | Glu118 forms a hydrogen bond with O6 of the second N-acetylglucosamine residue of the substrate. | electrostatic stabiliser |
| Asp100 | Asp60A | Asp-60 is in direct hydrogen bonding contact with O1 of the reducing-end GlcNAc residue (cleavage site) indicating that it is likely the primary catalytic residue. This is suggestive that it is this residue that acts as the nucleophile (inferred from similarity to other similar proteins). | covalent catalysis |
| Glu246 | Glu206A | Glu206 makes contact to the substrate through a bridging water molecule and is probably important for stabilisation of reaction intermediates. This residue may also act as the required general acid/base. | proton shuttle (general acid/base), electrostatic stabiliser |
*PDB label guide - RESx(y)B(C) - RES: Residue Name; x: Residue ID in PDB file;
y: Residue ID in PDB sequence if different from PDB file; B: PDB Chain;
C: Biological Assembly Chain if different from PDB. If label is "Not Found" it means this residue is not found in the reference PDB.
Chemical Components
References
- Kuhn P et al. (1995), J Biol Chem, 270, 29493-29497. Active Site and Oligosaccharide Recognition Residues of Peptide-N^4-(N-acetyl-beta-D-glucosaminyl)asparagine Amidase F. DOI:10.1074/jbc.270.49.29493. PMID:7493989.
- Kuhn P et al. (1994), Biochemistry, 33, 11699-11706. Crystal Structure of Peptide-N4-(N-acetyl-.beta.-D-glucosaminyl)asparagine amidase F at 2.2-.ANG. Resolution. DOI:10.1021/bi00205a005. PMID:7918386.
- Norris GE et al. (1994), Structure, 2, 1049-1059. The three-dimensional structure of PNGase F, a glycosylasparaginase from Flavobacterium meningosepticum. PMID:7881905.
Catalytic Residues Roles
| Residue | Roles |
|---|---|
| Asp60A | covalent catalysis |
| Glu206A | proton shuttle (general acid/base) |
| Glu118A | electrostatic stabiliser |
| Glu206A | electrostatic stabiliser |