1L16

STRUCTURAL ANALYSIS OF THE TEMPERATURE-SENSITIVE MUTANT OF BACTERIOPHAGE T4 LYSOZYME, GLYCINE 156 (RIGHT ARROW) ASPARTIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Observed: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural analysis of the temperature-sensitive mutant of bacteriophage T4 lysozyme, glycine 156----aspartic acid.

Gray, T.M.Matthews, B.W.

(1987) J Biol Chem 262: 16858-16864

  • DOI: 10.2210/pdb1l16/pdb
  • Primary Citation of Related Structures:  
    1L16

  • PubMed Abstract: 
  • The structure of the mutant of bacteriophage T4 lysozyme in which Gly-156 is replaced by aspartic acid is described. The lysozyme was isolated by screening for temperature-sensitive mutants and has a melting temperature at pH 6.5 that is 6.1 degrees ...

    The structure of the mutant of bacteriophage T4 lysozyme in which Gly-156 is replaced by aspartic acid is described. The lysozyme was isolated by screening for temperature-sensitive mutants and has a melting temperature at pH 6.5 that is 6.1 degrees C lower than wild type. The mutant structure is destabilized, in part, because Gly-156 has conformational angles (phi, psi) that are not optimal for a residue with a beta-carbon. High resolution crystallographic refinement of the mutant structure (R = 17.7% at 1.7 A resolution) shows that the Gly----Asp substitution does not significantly alter the configurational angles (phi, psi) but forces the backbone to move, as a whole, approximately 0.6 A away from its position in wild-type lysozyme. This induced strain weakens a hydrogen bond network that exists in the wild-type structure and also contributes to the reduced stability of the mutant lysozyme. The introduction of an acidic side chain reduces the overall charge on the molecule and thereby tends to increase the stability of the mutant structure relative to wild type. However, at neutral pH this generalized electrostatic stabilization is offset by specific electrostatic repulsion between Asp-156 and Asp-92. The activity of the mutant lysozyme is approximately 50% that of wild-type lysozyme. This reduction in activity might be due to introduction of a negative charge and/or perturbation of the surface of the molecule in the region that is assumed to interact with peptidoglycan substrates.


    Related Citations: 
    • Contributions of Hydrogen Bonds of Thr 157 to the Thermodynamic Stability of Phage T4 Lysozyme
      Alber, T., Dao-Pin, S., Wilson, K., Wozniak, J.A., Cook, S.P., Matthews, B.W.
      (1987) Nature 330: 41
    • Structural Studies of Mutants of the Lysozyme of Bacteriophage T4. The Temperature-Sensitive Mutant Protein Thr157 (Right Arrow) Ile
      Gruetter, M.G., Gray, T.M., Weaver, L.H., Alber, T., Wilson, K., Matthews, B.W.
      (1987) J Mol Biol 197: 315
    • Structure of Bacteriophage T4 Lysozyme Refined at 1.7 Angstroms Resolution
      Weaver, L.H., Matthews, B.W.
      (1987) J Mol Biol 193: 189
    • Temperature-Sensitive Mutations of Bacteriophage T4 Lysozyme Occur at Sites with Low Mobility and Low Solvent Accessibility in the Folded Protein
      Alber, T., Dao-Pin, S., Nye, J.A., Muchmore, D.C., Matthews, B.W.
      (1987) Biochemistry 26: 3754
    • Common Precursor of Lysozymes of Hen Egg-White and Bacteriophage T4
      Matthews, B.W., Gruetter, M.G., Anderson, W.F., Remington, S.J.
      (1981) Nature 290: 334
    • Crystallographic Determination of the Mode of Binding of Oligosaccharides to T4 Bacteriophage Lysozyme. Implications for the Mechanism of Catalysis
      Anderson, W.F., Gruetter, M.G., Remington, S.J., Weaver, L.H., Matthews, B.W.
      (1981) J Mol Biol 147: 523
    • Relation between Hen Egg White Lysozyme and Bacteriophage T4 Lysozyme. Evolutionary Implications
      Matthews, B.W., Remington, S.J., Gruetter, M.G., Anderson, W.F.
      (1981) J Mol Biol 147: 545
    • Structure of the Lysozyme from Bacteriophage T4, an Electron Density Map at 2.4 Angstroms Resolution
      Remington, S.J., Anderson, W.F., Owen, J., Teneyck, L.F., Grainger, C.T., Matthews, B.W.
      (1978) J Mol Biol 118: 81
    • Atomic Coordinates for T4 Phage Lysozyme
      Remington, S.J., Teneyck, L.F., Matthews, B.W.
      (1977) Biochem Biophys Res Commun 75: 265
    • Comparison of the Predicted and Observed Secondary Structure of T4 Phage Lysozyme
      Matthews, B.W.
      (1975) Biochim Biophys Acta 405: 442
    • The Three Dimensional Structure of the Lysozyme from Bacteriophage T4
      Matthews, B.W., Remington, S.J.
      (1974) Proc Natl Acad Sci U S A 71: 4178
    • Crystallographic Data for Lysozyme from Bacteriophage T4
      Matthews, B.W., Dahlquist, F.W., Maynard, A.Y.
      (1973) J Mol Biol 78: 575

    Organizational Affiliation

    Institute of Molecular Biology, University of Oregon, Eugene 97403.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
T4 LYSOZYMEA164Escherichia virus T4Mutation(s): 0 
Gene Names: E
EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Observed: 0.177 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61α = 90
b = 61β = 90
c = 97γ = 120
Software Package:
Software NamePurpose
TNTrefinement
AGROVATA / ROTAVATAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1988-04-16
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other
  • Version 1.4: 2020-07-22
    Changes: Data collection, Database references, Other, Refinement description