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Hydrolase PDB id
Protein chain
310 a.a.
Waters ×222
PDB id:
Name: Hydrolase
Title: Crystal structure of peptide-n(4)-(n-acetyl-beta-d- glucosaminyl) asparagine amidase at 2.2 angstroms resolution
Structure: Peptide-n(4)-(n-acetyl-beta-d-glucosaminyl) asparagine amidase f. Chain: a. Engineered: yes
Source: Elizabethkingia meningoseptica. Organism_taxid: 238
2.20Å     R-factor:   0.183    
Authors: P.Van Roey,P.Kuhn
Key ref:
P.Kuhn et al. (1994). Crystal structure of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F at 2.2-A resolution. Biochemistry, 33, 11699-11706. PubMed id: 7918386 DOI: 10.1021/bi00205a005
02-Jun-94     Release date:   30-Nov-94    
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Protein chain
Pfam   ArchSchema ?
P21163  (PNGF_ELIMR) -  Peptide-N(4)-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F
354 a.a.
310 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of an N(4)-(acetyl-beta-D-glucosaminyl)asparagine residue in which the N-acetyl-D-glucosamine residue may be further glycosylated, to yield a (substituted) N-acetyl-beta-D- glucosaminylamine and the peptide containing an aspartic residue.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   1 term 
  Biochemical function     catalytic activity     4 terms  


DOI no: 10.1021/bi00205a005 Biochemistry 33:11699-11706 (1994)
PubMed id: 7918386  
Crystal structure of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F at 2.2-A resolution.
P.Kuhn, A.L.Tarentino, T.H.Plummer, P.Van Roey.
Peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F (PNGase F) is an amidase that cleaves the beta-aspartylglucosylamine bond of asparagine-linked glycans. The 34.8-kDa (314 amino acids) enzyme has a very broad substrate specificity and is extensively used for studies of the structure and function of glycoproteins. Enzymatic activity of PNGase F requires recognition of both the peptide and the carbohydrate components of the substrate. Only limited information regarding the mechanism of action of the enzyme is available. The three-dimensional structure of PNGase F has been determined by X-ray crystallography at 2.2-A resolution. The protein folds into two domains comprising residues 1-137 and 143-314, respectively. Both domains have eight-stranded antiparallel beta-sandwich motifs that are very similar in geometry. Both sandwiches have parallel principal axes and lie side by side. The covalent link between the domains is located at the top end of the molecule. Extensive hydrogen-bonding contacts occur along the full length of the interface between the two domains. Three different areas, all at the interface between the two domains, have been identified as possible locations for the active site of the enzyme. These include a hydrophobic bowl of about 20 A in diameter on one surface of the molecule, a long polar cleft on the opposite side, and a cleft at the bottom, which is lined with large aromatic residues including eight tryptophans.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21374780 W.Huang, J.Li, and L.X.Wang (2011).
Unusual Transglycosylation Activity of Flavobacterium meningosepticum Endoglycosidases Enables Convergent Chemoenzymatic Synthesis of Core Fucosylated Complex N-Glycopeptides.
  Chembiochem, 12, 932-941.  
15574324 S.D.Benson, J.K.Bamford, D.H.Bamford, and R.M.Burnett (2004).
Does common architecture reveal a viral lineage spanning all three domains of life?
  Mol Cell, 16, 673-685.  
  9541410 J.Xuan, A.L.Tarentino, B.G.Grimwood, T.H.Plummer, T.Cui, C.Guan, and P.Van Roey (1998).
Crystal structure of glycosylasparaginase from Flavobacterium meningosepticum.
  Protein Sci, 7, 774-781.
PDB code: 1ayy
9241431 C.Chothia, T.Hubbard, S.Brenner, H.Barns, and A.Murzin (1997).
Protein folds in the all-beta and all-alpha classes.
  Annu Rev Biophys Biomol Struct, 26, 597-627.  
9341145 J.Q.Fan, and Y.C.Lee (1997).
Detailed studies on substrate structure requirements of glycoamidases A and F.
  J Biol Chem, 272, 27058-27064.  
9312552 N.Ftouhi-Paquin, C.R.Hauer, R.F.Stack, A.L.Tarentino, and T.H.Plummer (1997).
Molecular cloning, primary structure, and properties of a new glycoamidase from the fungus Aspergillus tubigensis.
  J Biol Chem, 272, 22960-22965.  
8846222 C.Oinonen, R.Tikkanen, J.Rouvinen, and L.Peltonen (1995).
Three-dimensional structure of human lysosomal aspartylglucosaminidase.
  Nat Struct Biol, 2, 1102-1108.
PDB codes: 1apy 1apz
8747464 D.D.Leonidas, B.L.Elbert, Z.Zhou, H.Leffler, S.J.Ackerman, and K.R.Acharya (1995).
Crystal structure of human Charcot-Leyden crystal protein, an eosinophil lysophospholipase, identifies it as a new member of the carbohydrate-binding family of galectins.
  Structure, 3, 1379-1393.
PDB code: 1lcl
7493989 P.Kuhn, C.Guan, T.Cui, A.L.Tarentino, T.H.Plummer, and P.Van Roey (1995).
Active site and oligosaccharide recognition residues of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F.
  J Biol Chem, 270, 29493-29497.
PDB code: 1pnf
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