1L35

STRUCTURE OF A THERMOSTABLE DISULFIDE-BRIDGE MUTANT OF PHAGE T4 LYSOZYME SHOWS THAT AN ENGINEERED CROSSLINK IN A FLEXIBLE REGION DOES NOT INCREASE THE RIGIDITY OF THE FOLDED PROTEIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of a thermostable disulfide-bridge mutant of phage T4 lysozyme shows that an engineered cross-link in a flexible region does not increase the rigidity of the folded protein.

Pjura, P.E.Matsumura, M.Wozniak, J.A.Matthews, B.W.

(1990) Biochemistry 29: 2592-2598

  • DOI: 10.1021/bi00462a023
  • Primary Citation of Related Structures:  
    1L35

  • PubMed Abstract: 
  • A disulfide bond introduced between amino acid positions 9 and 164 in phage T4 lysozyme has been shown to significantly increase the stability of the enzyme toward thermal denaturation [Matsumura, M., Becktel, W.J., Levitt, M., & Matthews, B. W. (1989) Proc ...

    A disulfide bond introduced between amino acid positions 9 and 164 in phage T4 lysozyme has been shown to significantly increase the stability of the enzyme toward thermal denaturation [Matsumura, M., Becktel, W.J., Levitt, M., & Matthews, B. W. (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 6562-6566]. To elucidate the structural features of the engineered disulfide, the crystal structure of the disulfide mutant has been determined at 1.8-A resolution. Residue 9 lies in the N-terminal alpha-helix, while residue 164 is located at the extreme C terminus of T4 lysozyme, which is the most mobile part of the molecule. The refined structure shows that the formation of the disulfide bond is accompanied by relatively large (approximately 2.5 A) localized shifts in C-terminal main-chain atoms. Comparison of the geometry of the engineered disulfide with those of naturally observed disulfides in proteins shows that the engineered bridge adopts a left-handed spiral conformation with a typical set of dihedral angles and C alpha-C alpha distance. The geometry of the engineered disulfide suggests that it is slightly more strained than the disulfide of oxidized dithiothreitol but that the strain is within the range observed in naturally occurring disulfides. The wild-type and cross-linked lysozymes have very similar overall crystallographic temperature factors, indicating that the introduction of the disulfide bond does not impose rigidity on the folded protein structure. In particular, residues 162-164 retain high mobility in the mutant structure, consistent with the idea that stabilization of the protein is due to the effect of the disulfide cross-link on the unfolded rather than the folded state.(ABSTRACT TRUNCATED AT 250 WORDS)


    Related Citations: 
    • Structural Studies of Mutants of T4 Lysozyme that Alter Hydrophobic Stabilization
      Matsumura, M., Wozniak, J.A., Dao-Pin, S., Matthews, B.W.
      () To be published --: --
    • High-Resolution Structure of the Temperature-Sensitive Mutant of Phage Lysozyme, Arg 96 (Right Arrow) His
      Weaver, L.H., Gray, T.M., Gruetter, M.G., Anderson, D.E., Wozniak, J.A., Dahlquist, F.W., Matthews, B.W.
      (1989) Biochemistry 28: 3793
    • Contributions of Left-Handed Helical Residues to the Structure and Stability of Bacteriophage T4 Lysozyme
      Nicholson, H., Soderlind, E., Tronrud, D.E., Matthews, B.W.
      (1989) J Mol Biol 210: 181
    • Hydrophobic Stabilization in T4 Lysozyme Determined Directly by Multiple Substitutions of Ile 3
      Matsumura, M., Becktel, W.J., Matthews, B.W.
      (1988) Nature 334: 406
    • Enhanced Protein Thermostability from Designed Mutations that Interact with Alpha-Helix Dipoles
      Nicholson, H., Becktel, W.J., Matthews, B.W.
      (1988) Nature 336: 651
    • Replacements of Pro86 in Phage T4 Lysozyme Extend an Alpha-Helix But Do not Alter Protein Stability
      Alber, T., Bell, J.A., Dao-Pin, S., Nicholson, H., Cook, J.A.Wozniak S., Matthews, B.W.
      (1988) Science 239: 631
    • Enhanced Protein Thermostability from Site-Directed Mutations that Decrease the Entropy of Unfolding
      Matthews, B.W., Nicholson, H., Becktel, W.J.
      (1987) Proc Natl Acad Sci U S A 84: 6663
    • Structural Analysis of the Temperature-Sensitive Mutant of Bacteriophage T4 Lysozyme, Glycine 156 (Right Arrow) Aspartic Acid
      Gray, T.M., Matthews, B.W.
      (1987) J Biol Chem 262: 16858
    • 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 and Department of Physics, 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
UniProt
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Observed: 0.157 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.2α = 90
b = 61.2β = 90
c = 96.9γ = 120
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1990-01-15
    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