Biological Assembly 1  

 3D View: Structure

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14707.65 
• Atom Count: 1028 
• Residue Count: 130 
• Unique protein chains: 1

1I1Z

MUTANT HUMAN LYSOZYME (Q86D)

• DOI: 10.2210/pdb1I1Z/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): 1 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å

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

• PubMed: 9852096 
• Primary Citation of Related Structures:  
  1I22, 1I20


• 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.

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Related Citations: 

• 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
• 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.USA 89: 6803
• 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.USA 86: 6903




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Organizational Affiliation: 

Central Laboratories for Key Technology, Kirin Brewery Co. Ltd., 1-13-5 Fukuura, Kanazawa-ku, Yokohama 236 Japan. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
LYSOZYME C	A	130	Homo sapiens	Mutation(s): 1  Gene Names: LYZ (LZM) EC: 3.2.1.17
Find proteins for P61626 (Homo sapiens) Go to Gene View: LYZ Go to UniProtKB:  P61626

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 56.620	α = 90.00
b = 60.820	β = 90.00
c = 33.830	γ = 90.00

Software Package:

Software Name	Purpose
SDMS	data scaling
SDMS	data reduction
TNT	refinement
TNT	phasing
SDMS	data collection

Structure Validation

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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance