Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 14665.53 
• Atom Count: 1027 
• Residue Count: 130 
• Unique protein chains: 1

2BQC

CONTRIBUTION OF HYDROPHOBIC EFFECT TO THE CONFORMATIONAL STABILITY OF HUMAN LYSOZYME

• DOI: 10.2210/pdb2BQC/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Saccharomyces cerevisiae
• Mutation(s): 3 


• Deposited: 1998-05-21 Released: 1998-08-12 
• Deposition Author(s): Takano, K., Yamagata, Y., Yutani, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Work: 0.168 

Literature

A general rule for the relationship between hydrophobic effect and conformational stability of a protein: stability and structure of a series of hydrophobic mutants of human lysozyme.

Takano, K., Yamagata, Y., Yutani, K.

(1998) J.Mol.Biol. 280: 749-761

• PubMed: 9677301 
• DOI: 10.1006/jmbi.1998.1906
• Primary Citation of Related Structures:  
  2BQO, 2BQN, 2BQM, 2BQL, 2BQK, 2BQJ, 2BQI, 2BQH, 2BQG, 2BQF, 2BQE, 2BQD, 2BQB, 2BQA


• PubMed Abstract: 
  

To get a general rule for the relationship between hydrophobic effect and conformational stability, five Ile to Val and nine Val to Ala mutants (3SS mutants) from 3SS (C77A/C95A) human lysozyme were constructed. As known from previous studies, the 3SS protein lacking a disulfide bond between Cys77 and Cys95 is destabilized by enthalpic factors, as revealed by a decrease of about 20 kJ/mol in the denaturation Gibbs energy change (DeltaG) value, as compared to the wild-type protein, which has four disulfide bonds. In this study, the stabilities and structures of the 3SS mutants were determined by differential scanning calorimetry and X-ray crystal analysis, respectively, and compared with those of the mutants (4SS mutants) from the wild-type (4SS) protein published previously. The stabilities of all the 3SS mutants, except for V110A-3SS were decreased as compared with that of the 3SS protein, coinciding with the results for the 4SS mutants. The change in the denaturation Gibbs energy change (DeltaDeltaG) values of the 3SS mutants relative to the 3SS protein at the denaturation temperature (49.2 degreesC) of the 3SS protein at pH 2.7 were similar to those of the equivalent 4SS mutants relative to the wild-type at 64.9 degreesC. The Delta DeltaG values of the 3SS mutants correlated with the changes in hydrophobic surface area exposed upon denaturation (Delta DeltaASAHP) for all of the hydrophobic residues when the effects of the secondary structure propensity were considered. This correlation is identical with that previously found for the 4SS mutants. The linear relation between Delta DeltaG and Delta DeltaASAHP for all of the hydrophobic residues with the same slope was found also for the mutants of T4 lysozyme already reported, indicating that this is a general relationship between changes in conformational stability and changes in ASA values of hydrophobic residues due to mutations.

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Related Citations: 

• Contribution of Water Molecules in the Interior of a Protein to the Conformational Stability
  Takano, K.,Funahashi, J.,Yamagata, Y.,Fujii, S.,Yutani, K.
  (1997) J.Mol.Biol. 274: 132
• Enthalpic Destabilization of a Mutant Human Lysozyme Lacking a Disulfide Bridge between Cysteine-77 and Cysteine-95
  Kuroki, R.,Inaka, K.,Taniyama, Y.,Kidokoro, S.,Matsushima, M.,Kikuchi, M.,Yutani, K.
  (1992) Biochemistry 31: 8323
• The Crystal Structure of a Mutant Human Lysozyme C77/95A with Increased Secretion Efficiency in Yeast
  Inaka, K.,Taniyama, Y.,Kikuchi, M.,Morikawa, K.,Matsushima, M.
  (1991) J.Biol.Chem. 266: 12599
• Contribution of the Hydrophobic Effect to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analyses of the Nine Valine to Alanine Mutants
  Takano, K.,Yamagata, Y.,Fujii, S.,Yutani, K.
  (1997) Biochemistry 36: 688
• The Structure, Stability, and Folding Process of Amyloidogenic Mutant Human Lysozyme
  Funahashi, J.,Takano, K.,Ogasahara, K.,Yamagata, Y.,Yutani, K.
  (1996) J.Biochem.(Tokyo) 120: 1216
• Contribution of Hydrophobic Residues to the Stability of Human Lysozyme: Calorimetric Studies and X-Ray Structural Analysis of the Five Isoleucine to Valine Mutants
  Takano, K.,Ogasahara, K.,Kaneda, H.,Yamagata, Y.,Fujii, S.,Kanaya, E.,Kikuchi, M.,Oobatake, M.,Yutani, K.
  (1995) J.Mol.Biol. 254: 62
• Contribution of Hydrogen Bonds to the Conformational Stability of Human Lysozyme: Calorimetry and X-Ray Analysis of Six Tyrosine--> Phenylalanine Mutants
  Yamagata, Y.,Kubota, M.,Sumikawa, Y.,Funahashi, J.,Takano, K.,Fujii, S.,Yutani, K.
  (1998) Biochemistry 37: 9355




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Organizational Affiliation: 

Institute for Protein Research, Osaka University, Yamadaoka, Suita, 565-0871, Japan.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
LYSOZYME	A	130	Homo sapiens	Mutation(s): 3  Gene Names: LYZ (LZM) EC: 3.2.1.17
Find proteins for P61626 (Homo sapiens) Go to Gene View: LYZ Go to UniProtKB:  P61626

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Work: 0.168 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 56.330	α = 90.00
b = 60.820	β = 90.00
c = 33.510	γ = 90.00

Software Package:

Software Name	Purpose
PROCESS	data scaling
X-PLOR	phasing
X-PLOR	refinement
PROCESS	data collection
X-PLOR	model building
PROCESS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-05-21 
• Released Date: 1998-08-12 
• Deposition Author(s): Takano, K., Yamagata, Y., Yutani, K.

Revision History 

• Version 1.0: 1998-08-12
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance