1L36

TOWARD A SIMPLIFICATION OF THE PROTEIN FOLDING PROBLEM: A STABILIZING POLYALANINE ALPHA-HELIX ENGINEERED IN T4 LYSOZYME


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Toward a simplification of the protein folding problem: a stabilizing polyalanine alpha-helix engineered in T4 lysozyme.

Zhang, X.J.Baase, W.A.Matthews, B.W.

(1991) Biochemistry 30: 2012-2017


  • PubMed Abstract: 
  • In an attempt to simplify the protein folding problem, and also to further investigate the role of alanine as a helix-stabilizing residue, a series of alanines was introduced within the alpha-helix that includes residues 126-134 of T4 lysozyme. In wi ...

    In an attempt to simplify the protein folding problem, and also to further investigate the role of alanine as a helix-stabilizing residue, a series of alanines was introduced within the alpha-helix that includes residues 126-134 of T4 lysozyme. In wild-type lysozyme this alpha-helix contains alanine residues at positions 129, 130, and 134. Mutant lysozymes with alanines substituted at positions 128, 131, 132, and 133, either as single substitutions or in selected combinations, were constructed by oligonucleotide-directed mutagenesis. With the exception of the replacement of Leu 133, which is buried within the hydrophobic core of the protein, all the variants were more stable than wild-type lysozyme. The variant with alanines substituted at positions 128, 131, and 132 (E128A/V131A/N132A), which incorporates the sequence Ala 128-Ala 129-Ala 130-Ala 131-Ala 132-Leu 133-Ala 134, has a melting temperature 3.3 degrees C above that of wild-type lysozyme. Determination of the crystal structure of this mutant lysozyme shows that the replacement of Glu 128, Val 131, and Asn 132 with alanine causes alpha-helix 126-134 to rotate 3.4 degrees about an axis parallel to its own axis. This rotation seems to be triggered primarily by the loss of a hydrogen bond between Asn 132 and Ser 117 and is associated with the repacking of several side chains at the interface between alpha-helix 126-134 and the adjacent alpha-helix 115-122.(ABSTRACT TRUNCATED AT 250 WORDS)


    Related Citations: 
    • 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
      Pjura, P.E.,Matsumura, M.,Wozniak, J.A.,Matthews, B.W.
      (1990) Biochemistry 29: 2592
    • Enhanced Protein Thermostability from Designed Mutations that Interact with Alpha-Helix Dipoles
      Nicholson, H.,Becktel, W.J.,Matthews, B.W.
      (1988) Nature 336: 651
    • Crystallographic Data for Lysozyme from Bacteriophage T4
      Matthews, B.W.,Dahlquist, F.W.,Maynard, A.Y.
      (1973) J.Mol.Biol. 78: 575
    • 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.USA 84: 6663
    • Tolerance of T4 Lysozyme to Multiple Xaa (Right Arrow) Ala Substitutions: A Polyalanine Alpha-Helix Containing Ten Consecutive Alanines
      Heinz, D.W.,Baase, W.A.,Matthews, B.W.
      () TO BE PUBLISHED --: --
    • Structural Studies of Mutants of T4 Lysozyme that Alter Hydrophobic Stabilization
      Matsumura, M.,Wozniak, J.A.,Dao-Pin, S.,Matthews, B.W.
      (1989) J.Biol.Chem. 264: 16059
    • Cumulative Site-Directed Charge-Change Replacements in Bacteriophage T4 Lysozyme Suggest that Long-Range Electrostatic Interactions Contribute Little to Protein Stability
      Dao-Pin, S.,Soderlind, E.,Baase, W.A.,Wozniak, J.A.,Sauer, U.,Matthews, B.W.
      (1991) J.Mol.Biol. 221: 873
    • Analysis of the Interaction between Charged Side Chains and the Alpha-Helix Dipole Using Designed Thermostable Mutants of Phage T4 Lysozyme
      Nicholson, H.,Anderson, D.E.,Dao-Pin, S.,Matthews, B.W.
      (1991) Biochemistry 30: 9816
    • 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
    • Structural and Thermodynamic Analysis of the Packing of Two Alpha-Helices in Bacteriophage T4 Lysozyme
      Daopin, S.,Alber, T.,Baase, W.A.,Wozniak, J.A.,Matthews, B.W.
      (1991) J.Mol.Biol. 221: 647
    • 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
    • Tolerance of T4 Lysozyme to Proline Substitutions within the Long Interdomain Alpha-Helix Illustrates the Adaptability of Proteins to Potentially Destabilizing Lesions
      Sauer, U.H.,Dao-Pin, S.,Matthews, B.W.
      () TO BE PUBLISHED --: --
    • Contributions of Engineered Surface Salt Bridges to the Stability of T4 Lysozyme Determined by Directed Mutagenesis
      Dao-Pin, S.,Sauer, U.,Nicholson, H.,Matthews, B.W.
      (1991) Biochemistry 30: 7142
    • 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
    • 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
    • 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
    • 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
    • Atomic Coordinates for T4 Phage Lysozyme
      Remington, S.J.,Teneyck, L.F.,Matthews, B.W.
      (1977) Biochem.Biophys.Res.Commun. 75: 265
    • 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
    • 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
    • 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
    • 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
    • Nicholson, H.,Becktel, W.,Matthews, B.W.
      () TO BE PUBLISHED --: --
    • Structure of Bacteriophage T4 Lysozyme Refined at 1.7 Angstroms Resolution
      Weaver, L.H.,Matthews, B.W.
      (1987) J.Mol.Biol. 193: 189
    • 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
    • The Structural and Thermodynamic Consequences of Burying a Charged Residue within the Hydrophobic Core of T4 Lysozyme
      Daopin, S.,Anderson, E.,Baase, W.,Dahlquist, F.W.,Matthews, B.W.
      () TO BE PUBLISHED --: --
    • Multiple Stabilizing Alanine Replacements within Alpha-Helix 126-134 of T4 Lysozyme Have Independent, Additive Effects on Both Structure and Stability
      Zhang, X.-J.,Baase, W.A.,Matthews, B.W.
      () TO BE PUBLISHED --: --
    • The Three Dimensional Structure of the Lysozyme from Bacteriophage T4
      Matthews, B.W.,Remington, S.J.
      (1974) Proc.Natl.Acad.Sci.USA 71: 4178
    • Comparison of the Predicted and Observed Secondary Structure of T4 Phage Lysozyme
      Matthews, B.W.
      (1975) Biochim.Biophys.Acta 405: 442


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
LYSOZYME
A
164Enterobacteria phage T4Mutation(s): 0 
Gene Names: E
EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4)
Go to UniProtKB:  P00720
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
BME
Query on BME

Download SDF File 
Download CCD File 
A
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 61.300α = 90.00
b = 61.300β = 90.00
c = 96.300γ = 120.00
Software Package:
Software NamePurpose
TNTrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1991-10-15
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other