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 1.2 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: 10.1074/jbc.273.51.34310
  • Structures With Same Primary Citation

  • 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, ...

    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.


    Related Citations: 
    • Thermodynamic changes in the binding of Ca2+ to a mutant human lysozyme (D86/92). Enthalpy-entropy compensation observed upon Ca2+ binding to proteins.
      Kuroki, R., Nitta, K., Yutani, K.
      (1992) J Biol Chem 267: 24297
    • Entropic Stabilization of a Mutant Human Lysozyme Induced by Calcium Binding
      Kuroki, R., Kawakita, S., Nakamura, H., Yutani, K.
      (1992) Proc Natl Acad Sci U S A 89: 6803
    • Crystal Structure of the Apo- and Holomutant Human Lysozymes with an Introduced Ca2+ Binding Site
      Inaka, K., Kuroki, R., Kikuchi, M., Matsushima, M.
      (1991) J Biol Chem 266: 20666
    • Design and Creation of a Ca2+ Binding Site in Human Lysozyme to Enhance Structural Stability
      Kuroki, R., Taniyam, Y., Seko, C., Nakamura, H., Kikuchi, M., Ikehara, M.
      (1989) Proc Natl Acad Sci U S A 86: 6903

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSOZYME C
A
130Homo sapiensMutation(s): 1 
Gene Names: LYZLZM
EC: 3.2.2.17 (PDB Primary Data), 3.2.1.17 (UniProt)
Find proteins for P61626 (Homo sapiens)
Go to UniProtKB:  P61626
NIH Common Fund Data Resources
PHAROS  P61626
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

  • Deposited Date: 2001-02-05 
  • Released Date: 2001-02-28 
  • Deposition Author(s): Kuroki, R.

Revision History 

  • 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