3GXR

The crystal structure of g-type lysozyme from Atlantic cod (Gadus morhua L.) in complex with NAG oligomers sheds new light on substrate binding and the catalytic mechanism. Structure with NAG to 1.7

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Crystal structures of g-type lysozyme from Atlantic cod shed new light on substrate binding and the catalytic mechanism.

Helland, R., Larsen, R.L., Finstad, S., Kyomuhendo, P., Larsen, A.N.

(2009) Cell.Mol.Life Sci. 66: 2585-2598

  • DOI: 10.1007/s00018-009-0063-x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Crystal structures of Atlantic cod lysozyme have been solved with and without ligand bound in the active site to 1.7 and 1.9 A resolution, respectively. The structures reveal the presence of NAG in the substrate binding sites at both sides of the cat ...

    Crystal structures of Atlantic cod lysozyme have been solved with and without ligand bound in the active site to 1.7 and 1.9 A resolution, respectively. The structures reveal the presence of NAG in the substrate binding sites at both sides of the catalytic Glu73, hence allowing the first crystallographic description of the goose-type (g-type) lysozyme E-G binding sites. In addition, two aspartic acid residues suggested to participate in catalysis (Asp101 and Asp90) were mutated to alanine. Muramidase activity data for two single mutants and one double mutant demonstrates that both residues are involved in catalysis, but Asp101 is the more critical of the two. The structures and activity data suggest that a water molecule is the nucleophile completing the catalytic reaction, and the roles of the aspartic acids are to ensure proper positioning of the catalytic water.

    Organizational Affiliation: 

    Department of Chemistry, The Norwegian Structural Biology Centre, University of Tromsø, 9037 Tromsø, Norway. Ronny.Helland@uit.no




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Goose-type lysozyme 1
A, B, C, D
187Gadus morhuaMutation(s): 0 
Find proteins for B9TU22 (Gadus morhua)
Go to UniProtKB:  B9TU22
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download SDF File 
Download CCD File 
A, B, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.204 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 110.190α = 90.00
b = 75.520β = 93.25
c = 78.290γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
MOLREPphasing
MAR345data collection
REFMACrefinement
SCALAdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.2: 2017-11-01
    Type: Refinement description