1B5W

CONTRIBUTION OF HYDROGEN BONDS TO THE CONFORMATIONAL STABILITY OF HUMAN LYSOZYME: CALORIMETRY AND X-RAY ANALYSIS OF SIX SER->ALA MUTANTS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Contribution of hydrogen bonds to the conformational stability of human lysozyme: calorimetry and X-ray analysis of six Ser --> Ala mutants.

Takano, K.Yamagata, Y.Kubota, M.Funahashi, J.Fujii, S.Yutani, K.

(1999) Biochemistry 38: 6623-6629

  • DOI: 10.1021/bi9901228
  • Primary Citation of Related Structures:  1B5U, 1B5V, 1B5X, 1B5Y, 1B5Z

  • PubMed Abstract: 
  • To further examine the contribution of hydrogen bonds to the conformational stability of the human lysozyme, six Ser to Ala mutants were constructed. The thermodynamic parameters for denaturation of these six Ser mutant proteins were investigated by ...

    To further examine the contribution of hydrogen bonds to the conformational stability of the human lysozyme, six Ser to Ala mutants were constructed. The thermodynamic parameters for denaturation of these six Ser mutant proteins were investigated by differential scanning calorimetry (DSC), and the crystal structures were determined by X-ray analysis. The denaturation Gibbs energy (DeltaG) of the Ser mutant proteins was changed from 2.0 to -5.7 kJ/mol, compared to that of the wild-type protein. With an analysis in which some factors that affected the stability due to mutation were considered, the contribution of hydrogen bonds to the stability (Delta DeltaGHB) was extracted on the basis of the structures of the mutant proteins. The results showed that hydrogen bonds between protein atoms and between a protein atom and a water bound with the protein molecule favorably contribute to the protein stability. The net contribution of one intramolecular hydrogen bond to protein stability (DeltaGHB) was 8.9 +/- 2.6 kJ/mol on average. However, the contribution to the protein stability of hydrogen bonds between a protein atom and a bound water molecule was smaller than that for a bond between protein atoms.


    Related Citations: 
    • Contribution of Hydrogen Bonds to the Conformational Stability of Human Lysozyme: Calorimetry and X-Ray Analysis of Six Tyr->Phe Mutants
      Yamagata, Y.,Kubota, M.,Sumikawa, Y.,Funahashi, J.,Takano, K.,Fujii, S.,Yutani, K.
      (1998) Biochemistry 37: 9355
    • Contribution of Hydrophobic Effect Valine Mutants 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
    • 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.,Ogasawaha, K.,Kaneda, H.,Yamagata, Y.,Fujii, S.,Kanaya, E.,Kikuchi, M.,Oobatake, M.,Yutani, K.
      (1995) J.Mol.Biol. 254: 62
    • Contribution of Water Molecules in the Interior of a Protein to the Conformational Stability
      Takano, K.,Funahasihi, J.F.,Yamagata, Y.,Fujii, S.,Yutani, K.
      (1997) J.Mol.Biol. 274: 132
    • 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
    • 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


    Organizational Affiliation

    Institute for Protein Research, Osaka University, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (LYSOZYME)
A
130Homo sapiensGene 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.17 Å
  • R-Value Work: 0.155 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.570α = 90.00
b = 60.710β = 90.00
c = 33.520γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
SCALEPACKdata scaling
X-PLORmodel building
DENZOdata reduction
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-01-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance