1L75

MULTIPLE STABILIZING ALANINE REPLACEMENTS WITHIN ALPHA-HELIX 126-134 OF T4 LYSOZYME HAVE INDEPENDENT, ADDITIVE EFFECTS ON BOTH STRUCTURE AND STABILITY


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Multiple 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.

(1992) Protein Sci. 1: 761-776

  • DOI: 10.1002/pro.5560010608
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In a systematic attempt to identify residues important in the folding and stability of T4 lysozyme, five amino acids within alpha-helix 126-134 were substituted by alanine, either singly or in selected combinations. Together with three alanines alrea ...

    In a systematic attempt to identify residues important in the folding and stability of T4 lysozyme, five amino acids within alpha-helix 126-134 were substituted by alanine, either singly or in selected combinations. Together with three alanines already present in the wild-type structure this provided a set of mutant proteins with up to eight alanines in sequence. All the variants behaved normally, suggesting that the majority of residues in the alpha-helix are nonessential for the folding of T4 lysozyme. Of the five individual alanine substitutions it is inferred that four result in slightly increased protein stability and one, the replacement of a buried leucine with alanine, substantially decreased stability. The results support the idea that alanine is a residue of high helix propensity. The change in protein stability observed for each of the multiple mutants is approximately equal to the sum of the energies associated with each of the constituent substitutions. All of the variants could be crystallized isomorphously with wild-type lysozyme, and, with one trivial exception, their structures were determined at high resolution. Substitution of the largely solvent-exposed residues Asp 127, Glu 128, and Val 131 with alanine caused essentially no change in structure except at the immediate site of replacement. Substitutions of the partially buried Asn 132 and the buried Leu 133 with alanine were associated with modest (< or = 0.4 A) structural adjustments. The structural changes seen in the multiple mutants were essentially a combination of those seen in the constituent single replacements. The different replacements therefore act essentially independently not only so far as changes in energy are concerned but also in their effect on structure. The destabilizing replacement Leu 133-->Ala made alpha-helix 126-134 somewhat less regular. Incorporation of additional alanine replacements tended to make the helix more uniform. For the penta-alanine variant a distinct change occurred in a crystal-packing contact, and the "hinge-bending angle" between the amino- and carboxy-terminal domains changed by 3.6 degrees. This tends to confirm that such hinge-bending in T4 lysozyme is a low-energy conformational change.


    Related Citations: 
    • 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 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
    • Comparison of the Predicted and Observed Secondary Structure of T4 Phage Lysozyme
      Matthews, B.W.
      (1975) Biochim.Biophys.Acta 405: 442
    • 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
    • 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
    • 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
    • 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 --: --
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • Enhanced Protein Thermostability from Designed Mutations that Interact with Alpha-Helix Dipoles
      Nicholson, H.,Becktel, W.J.,Matthews, B.W.
      (1988) Nature 336: 651
    • Nicholson, H.,Becktel, W.,Matthews, B.W.
      () TO BE PUBLISHED --: --
    • Atomic Coordinates for T4 Phage Lysozyme
      Remington, S.J.,Teneyck, L.F.,Matthews, B.W.
      (1977) Biochem.Biophys.Res.Commun. 75: 265
    • 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
    • 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
    • Crystallographic Data for Lysozyme from Bacteriophage T4
      Matthews, B.W.,Dahlquist, F.W.,Maynard, A.Y.
      (1973) J.Mol.Biol. 78: 575
    • 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
    • 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 --: --
    • 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
    • The Three Dimensional Structure of the Lysozyme from Bacteriophage T4
      Matthews, B.W.,Remington, S.J.
      (1974) Proc.Natl.Acad.Sci.USA 71: 4178
    • 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
    • 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 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
    • 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


    Organizational Affiliation

    Institute of Molecular Biology, Howard Hughes Medical Institute, 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: 1.9 Å
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 61.100α = 90.00
b = 61.100β = 90.00
c = 93.400γ = 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: Version format compliance
  • Version 1.3: 2017-11-29
    Type: Derived calculations, Other