2Z2E

Crystal Structure of Canine Milk Lysozyme Stabilized against Non-enzymatic Deamidation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.413 
  • R-Value Work: 0.273 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Spontaneous asparaginyl deamidation of canine milk lysozyme under mild conditions

Nonaka, Y.Aizawa, T.Akieda, D.Yasui, M.Watanabe, M.Watanabe, N.Tanaka, I.Kamiya, M.Mizuguchi, M.Demura, M.Kawano, K.

(2008) Proteins 72: 313-322

  • DOI: 10.1002/prot.21927

  • PubMed Abstract: 
  • Asparaginyl deamidation is a common form of nonenzymatic degradation of proteins and peptides. As it introduces a negative charge spontaneously and irreversibly, charge heterogeneity can be accumulated in protein solution during purification, preserv ...

    Asparaginyl deamidation is a common form of nonenzymatic degradation of proteins and peptides. As it introduces a negative charge spontaneously and irreversibly, charge heterogeneity can be accumulated in protein solution during purification, preservation, and experiments. In this study, canine milk lysozyme (CML), a useful model for the study of the molten globule state, exhibited charge heterogeneity after sample purification. Four Asn residues in CML deamidated rapidly under mild conditions: pH 8.0 and 30 degrees C. Other than these residues, one Asn residue, which was stable in the native state, was labile to deamidation in the unfolded state. This suggests that the structural formation around Asn can suppress deamidation. Substitutions of these labile Asn residues to Gln residues prevented deamidation effectively. Because the substitutions did not disrupt the structural formation of the native and molten globule states, they will enable more precise analyses for physical and structural studies.


    Organizational Affiliation

    Graduate School of Science, Hokkaido University, Sapporo, Hokkaido, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C, milk isozyme
A, B
129Canis lupus familiarisMutation(s): 5 
EC: 3.2.1.17
Find proteins for P81708 (Canis lupus familiaris)
Go to UniProtKB:  P81708
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 0.413 
  • R-Value Work: 0.273 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 31.216α = 90.00
b = 31.216β = 90.00
c = 198.307γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
CrystalCleardata collection
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-11-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance