1L89

SIMILAR HYDROPHOBIC REPLACEMENTS OF LEU 99 AND PHE 153 WITHIN THE CORE OF T4 LYSOZYME HAVE DIFFERENT STRUCTURAL AND THERMODYNAMIC CONSEQUENCES


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Similar hydrophobic replacements of Leu99 and Phe153 within the core of T4 lysozyme have different structural and thermodynamic consequences.

Eriksson, A.E.Baase, W.A.Matthews, B.W.

(1993) J Mol Biol 229: 747-769

  • DOI: https://doi.org/10.1006/jmbi.1993.1077
  • Primary Citation of Related Structures:  
    1L85, 1L86, 1L87, 1L88, 1L89, 1L90, 1L91, 1L92, 1L93, 1L94, 1L95

  • PubMed Abstract: 

    Two bulky amino acids within the core of phage T4 lysozyme have each been replaced in turn with a series of hydrophobic amino acids. In one set of experiments, Leu99 was replaced with Phe, Met, Ile, Val and Ala. In the second series, Phe153 was replaced with Leu, Met, Ile, Val and Ala. The double mutant in which both Leu99 and Phe153 were replaced with alanine was also constructed. The change in stability of the protein associated with each substitution and the crystal structure of each variant have been determined. In the case of replacements at position 99 the protein behaves in a relatively rigid manner, and changes very little in response to substitutions. In contrast, the protein is more flexible and adjusts much more in response to substitutions of Phe153. In both cases there is a roughly linear dependence between the stability of the mutant protein relative to wild-type (delta delta G) and the difference in the hydrophobic strength of the amino acids involved in the substitution based on solvent transfer measurements (delta delta Gtr). The change in delta delta G is, however, much greater than delta delta Gtr. For the Phe153 replacements the discrepancy is about 1.9-fold, while for the Leu99 series it is about 2.6-fold. Mutants such as Leu99-->Ala, for which the protein remains essentially rigid, tend to create larger cavities and so incur a larger energy of destabilization. Mutants such as Phe153-->Ala, for which the protein structure tends to relax, result in smaller cavities and so are less destabilized. Mutants L99I and L99V are less stable than expected from considerations of transfer free energy and cavity formation due to introduced strain caused by the replacement of Leu99 with a residue of different shape. Mutant F153L is more stable than the reference wild-type, even though the transfer free energy of Leu is less than that of Phe. The increase in stability is apparently due to torsional strain in the side-chain of Phe153 that is present in wild-type lysozyme, but is relieved in the mutant structure.


  • Organizational Affiliation

    Institute of Molecular Biology, Howard Hughes Medical Institute, Eugene, OR.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
T4 LYSOZYME164Tequatrovirus T4Mutation(s): 0 
EC: 3.2.1.17
UniProt
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00720
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.171 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.4α = 90
b = 61.4β = 90
c = 95.6γ = 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: 1993-10-31
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations