1L21

CONTRIBUTIONS OF LEFT-HANDED HELICAL RESIDUES TO THE STRUCTURE AND STABILITY OF BACTERIOPHAGE T4 LYSOZYME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 181-193

  • DOI: 10.1016/0022-2836(89)90299-4
  • Primary Citation of Related Structures:  
    1L22, 1L21, 1L33

  • PubMed Abstract: 
  • Non-glycine residues in proteins are rarely observed to have "left-handed helical" conformations. For glycine, however, this conformation is common. To determine the contributions of left-handed helical residues to the stability of a protein, two suc ...

    Non-glycine residues in proteins are rarely observed to have "left-handed helical" conformations. For glycine, however, this conformation is common. To determine the contributions of left-handed helical residues to the stability of a protein, two such residues in phage T4 lysozyme, Asn55 and Lys124, were replaced with glycine. The mutant proteins fold normally and are fully active, showing that left-handed non-glycine residues, although rare, do not have an indispensable role in the folding of the protein or in its activity. The thermodynamic stability of the Lys124 to Gly variant is essentially identical with that of wild-type lysozyme. The Asn55 to Gly mutant protein is marginally less stable (0.5 kcal/mol). These results indicate that the conformational energy of a glycine and a non-glycine residue in the left-handed helical conformation are very similar. This is consistent with some theoretical energy distributions, but is inconsistent with others, which suggest that replacements of the sort described here might increase the stability of the protein by up to 5 kcal/mol. Crystallographic analysis of the mutant proteins shows that the backbone conformation of the Lys124 to Gly variant is essentially identical with that of the wild-type structure. In the case of the Asn55 to Gly replacement, however, the (phi, psi) values of residue 55 change by about 20 degrees. This suggests that the energy minimum for left-handed glycine residues is not the same as that for non-glycine residues. This is strongly indicated also by a survey of accurately determined protein crystal structures, which suggests that the energy minimum for left-handed glycine residues is near (phi = 90 degrees, psi = 0 degrees), whereas that for non-glycine residues is close to (phi = 60 degrees, psi = 30 degrees). This apparent energy minimum for glycine is not clearly predicted by any of the theoretical (phi, psi) energy contour maps.


    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
    • 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, 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: 1.85 Å
  • R-Value Observed: 0.173 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.1α = 90
b = 61.1β = 90
c = 97γ = 120
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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