9LYZ

X-RAY CRYSTALLOGRAPHY OF THE BINDING OF THE BACTERIAL CELL WALL TRISACCHARIDE NAM-NAG-NAM TO LYSOZYME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.230 

wwPDB Validation   3D Report Full Report



Literature

X-ray crystallography of the binding of the bacterial cell wall trisaccharide NAM-NAG-NAM to lysozyme.

Kelly, J.A.Sielecki, A.R.Sykes, B.D.James, M.N.Phillips, D.C.

(1979) Nature 282: 875-878

  • DOI: 10.1038/282875a0
  • Primary Citation of Related Structures:  
    9LYZ

  • PubMed Abstract: 
  • Hen egg white lysozyme was the first enzyme whose structure was determined by X-ray crystallography. The proposed mechanism based on this structure involves the distortion of the saccharide residue (2-acetamido-2-deoxy-D-muramic acid, NAM) in the natural ...

    Hen egg white lysozyme was the first enzyme whose structure was determined by X-ray crystallography. The proposed mechanism based on this structure involves the distortion of the saccharide residue (2-acetamido-2-deoxy-D-muramic acid, NAM) in the natural substrate (an alternating beta (1 leads to 4) linked oligomer of 2-acetamido-2-deoxy-D-glucose (NAG) and NAM residues) bound to site D in the binding cleft. The importance of substrate distortion has prompted numerous enzymatic, chemical, theoretical, and physical studies, but there is little direct crystallographic evidence on the conformation of a NAM residue bound at site D. We now present the X-ray structure of the non-hydrolysed trisaccharide NAM-NAG-NAM bound in subsites B, C, D. Our interpretation of the 2.5-A resolution difference map does not involve distortion of this residue in site D. Comparison with the structure of the delta-lactone derived from tetra N-acetylchitotetraose (NAG)3NAL) bound to lysozyme suggests we may be looking at a Michaelis complex.


    Organizational Affiliation

    Institute for Experimental Virology, Twincore Centre for Experimental and Clinical Infection Research, Hannover, Germany krey.thomas@mh-hannover.de christine.goffinet@twincore.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HEN EGG WHITE LYSOZYME A129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Explore P00698 
Go to UniProtKB:  P00698
Protein Feature View
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
N-acetyl-beta-muramic acid-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-N-acetyl-beta-muramic acid
B
3 N/A Oligosaccharides Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Work: 0.230 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.97α = 90
b = 78.97β = 90
c = 38.25γ = 90

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1980-02-27
    Type: Initial release
  • Version 1.1: 2011-06-03
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-07-27
    Changes: Non-polymer description, Other
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary