1H6M

Covalent glycosyl-enzyme intermediate of hen egg white lysozyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Catalysis by Hen Egg-White Lysozyme Proceeds Via a Covalent Intermediate

Vocadlo, D.J.Davies, G.J.Laine, R.Withers, S.G.

(2001) Nature 412: 835

  • DOI: 10.1038/35090602

  • PubMed Abstract: 
  • Hen egg-white lysozyme (HEWL) was the first enzyme to have its three-dimensional structure determined by X-ray diffraction techniques. A catalytic mechanism, featuring a long-lived oxocarbenium-ion intermediate, was proposed on the basis of model-bui ...

    Hen egg-white lysozyme (HEWL) was the first enzyme to have its three-dimensional structure determined by X-ray diffraction techniques. A catalytic mechanism, featuring a long-lived oxocarbenium-ion intermediate, was proposed on the basis of model-building studies. The 'Phillips' mechanism is widely held as the paradigm for the catalytic mechanism of beta-glycosidases that cleave glycosidic linkages with net retention of configuration of the anomeric centre. Studies with other retaining beta-glycosidases, however, provide strong evidence pointing to a common mechanism for these enzymes that involves a covalent glycosyl-enzyme intermediate, as previously postulated. Here we show, in three different cases using electrospray ionization mass spectrometry, a catalytically competent covalent glycosyl-enzyme intermediate during the catalytic cycle of HEWL. We also show the three-dimensional structure of this intermediate as determined by X-ray diffraction. We formulate a general catalytic mechanism for all retaining beta-glycosidases that includes substrate distortion, formation of a covalent intermediate, and the electrophilic migration of C1 along the reaction coordinate.


    Related Citations: 
    • Site Directed Mutagenesis of the Catalytic Residues Asp-52 and Glu-35 of Chicken Egg White Lysozyme
      Malcolm, B.A.,Rosenberg, S.,Corey, M.J.,Allen, J.S.,Debaetselier, A.,Kirsch, J.F.
      (1989) Proc.Natl.Acad.Sci.USA 86: 133
    • Lysozyme Revisited: Crystallographic Evidence for Distortion of an N-Acetylmuramic Residue Bound in Subsite D
      Strydnaka, N.C.J.,James, M.N.G.
      (1991) J.Mol.Biol. 220: 401
    • Structure of Hen Egg-White Lysozyme: A Three Dimensional Fourier Analysis at 2.0A Resolution
      Blake, C.C.F.,Koenig, D.F.,Mair, G.A.,North, A.C.T.,Phillips, D.C.,Sarma, V.R.
      (1965) Nature 206: 757


    Organizational Affiliation

    Protein Engineering Network of Centres of Excellence and the Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSOZYME C
A
129Gallus gallusMutation(s): 1 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G2F
Query on G2F

Download SDF File 
Download CCD File 
A
2-deoxy-2-fluoro-alpha-D-glucopyranose
C6 H11 F O5
ZCXUVYAZINUVJD-UKFBFLRUSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.64 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.170 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 78.632α = 90.00
b = 78.632β = 90.00
c = 36.700γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CCP4phasing
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-08-30
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance