1I1Z

MUTANT HUMAN LYSOZYME (Q86D)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.161 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural and thermodynamic responses of mutations at a Ca2+ binding site engineered into human lysozyme.

Kuroki, R.Yutani, K.

(1998) J Biol Chem 273: 34310-34315

  • DOI: https://doi.org/10.1074/jbc.273.51.34310
  • Primary Citation of Related Structures:  
    1I1Z, 1I20, 1I22

  • PubMed Abstract: 

    Structural determinants of Ca2+ binding sites within proteins typically comprise several acidic residues in appropriate juxtaposition. Three residues (Ala-83, Gln-86, and Ala-92) in human lysozyme are characteristically mutated to Lys, Asp, and Asp, respectively, in natural Ca2+ binding lysozymes and alpha-lactalbumins. The effects of these mutations on the stability and Ca2+ binding properties of human lysozyme were investigated using calorimetry and were interpreted with crystal structures. The double mutant, in which Glu-86 and Ala-92 were replaced with Asp, clearly showed Ca2+ binding affinity, whereas neither point mutant showed Ca2+ affinity, indicating that both residues are essential. The further mutation of Ala-83 --> Lys did not affect the Ca2+ binding of the double mutant. The point mutations Ala-83 --> Lys and Glu-86 --> Asp did not affect the stability, whereas the mutation Ala-92 --> Asp was about 1.3 kcal/mol less stable. Structural analyses showed that both Asp-86 and Lys-83 were exposed to solvent. Side chains of Asp-86 and Asp-91 were rotated in opposite directions about chi1 angle, as if to reduce the electrostatic repulsion. The charged amino acids at the Ca2+ binding site did not significantly affect stability of the protein, possibly because of the local conformational change of the side chains.


  • Organizational Affiliation

    Central Laboratories for Key Technology, Kirin Brewery Co. Ltd., 1-13-5 Fukuura, Kanazawa-ku, Yokohama 236 Japan. r-kuroki@kirin.co.jp


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LYSOZYME C130Homo sapiensMutation(s): 1 
EC: 3.2.2.17
UniProt & NIH Common Fund Data Resources
Find proteins for P61626 (Homo sapiens)
Explore P61626 
Go to UniProtKB:  P61626
PHAROS:  P61626
GTEx:  ENSG00000090382 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61626
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.161 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.62α = 90
b = 60.82β = 90
c = 33.83γ = 90
Software Package:
Software NamePurpose
SDMSdata collection
SDMSdata reduction
TNTrefinement
SDMSdata scaling
TNTphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2001-02-28 
  • Deposition Author(s): Kuroki, R.

Revision History  (Full details and data files)

  • Version 1.0: 2001-02-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations