1L76

TOLERANCE OF T4 LYSOZYME TO PROLINE SUBSTITUTIONS WITHIN THE LONG INTERDOMAIN ALPHA-HELIX ILLUSTRATES THE ADAPTABILITY OF PROTEINS TO POTENTIALLY DESTABILIZING LESIONS


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

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.San, D.P.Matthews, B.W.

(1992) J.Biol.Chem. 267: 2393-2399


  • PubMed Abstract: 
  • To investigate the ability of a protein to accommodate potentially destabilizing amino acid substitutions, and also to investigate the steric requirements for catalysis, proline was substituted at different sites within the long alpha-helix that conn ...

    To investigate the ability of a protein to accommodate potentially destabilizing amino acid substitutions, and also to investigate the steric requirements for catalysis, proline was substituted at different sites within the long alpha-helix that connects the amino-terminal and carboxyl-terminal domains of T4 lysozyme. Of the four substitutions attempted, three yielded folded, functional proteins. The catalytic activities of these three mutant proteins (Q69P, D72P, and A74P) were 60-90% that of wild-type. Their melting temperatures were 7-12 degrees C less than that of wild-type at pH 6.5. Mutant D72P formed crystals isomorphous with wild-type allowing the structure to be determined at high resolution. In the crystal structure of wild-type lysozyme the interdomain alpha-helix has an overall bend angle of 8.5 degrees. In the mutant structure the introduction of the proline causes this bend angle to increase to 14 degrees and also causes a corresponding rotation of 5.5 degrees of carboxyl-terminal domain relative to the amino-terminal one. Except for the immediate location of the proline substitution there is very little change in the geometry of the interdomain alpha-helix. The results support the view that protein structures are adaptable and can compensate for potentially destabilizing amino acid substitutions. The results also suggest that the precise shape of the active site cleft of T4 lysozyme is not critical for catalysis.


    Related Citations: 
    • 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
    • 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
    • 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
    • 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
    • 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
    • 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
    • Comparison of the Predicted and Observed Secondary Structure of T4 Phage Lysozyme
      Matthews, B.W.
      (1975) Biochim.Biophys.Acta 405: 442
    • 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
    • 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
    • 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
    • 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
    • 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 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
    • 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
    • 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 --: --
    • 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
    • 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
    • The Three Dimensional Structure of the Lysozyme from Bacteriophage T4
      Matthews, B.W.,Remington, S.J.
      (1974) Proc.Natl.Acad.Sci.USA 71: 4178
    • 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 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
    • 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
    • Structure of Bacteriophage T4 Lysozyme Refined at 1.7 Angstroms Resolution
      Weaver, L.H.,Matthews, B.W.
      (1987) J.Mol.Biol. 193: 189


    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 = 60.770α = 90.00
b = 60.770β = 90.00
c = 98.620γ = 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