1PNG

CRYSTAL STRUCTURE OF PEPTIDE-N(4)-(N-ACETYL-BETA-D-GLUCOSAMINYL) ASPARAGINE AMIDASE AT 2.2 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of peptide-N4-(N-acetyl-beta-D-glucosaminyl)asparagine amidase F at 2.2-A resolution.

Kuhn, P.Tarentino, A.L.Plummer Jr., T.H.Van Roey, P.

(1994) Biochemistry 33: 11699-11706


  • PubMed Abstract: 
  • 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 ...

    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.


    Related Citations: 
    • Crystallization and Preliminary Crystallographic Analysis of Peptide-N(4)-(N-Acetyl-Beta-D-Glucosaminyl) Asparagine Amidase (Pngasef)
      Kuhn, P.,Tarentino, A.L.,Plummer Junior, T.H.,Van Roey, P.
      (1994) J.Mol.Biol. 241: 622


    Organizational Affiliation

    Wadsworth Center, New York State Department of Health, Albany 12201-0509.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PEPTIDE-N(4)-(N-ACETYL-BETA-D-GLUCOSAMINYL)ASPARAGINE AMIDASE F
A
314Elizabethkingia miricolaGene Names: ngl (png)
EC: 3.5.1.52
Find proteins for P21163 (Elizabethkingia miricola)
Go to UniProtKB:  P21163
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Work: 0.183 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 87.160α = 90.00
b = 125.100β = 90.00
c = 79.330γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1994-06-02 
  • Released Date: 1994-11-30 
  • Deposition Author(s): Van Roey, P., Kuhn, P.

Revision History 

  • Version 1.0: 1994-11-30
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other