Evaluation at atomic resolution of the role of strain in destabilizing the temperature-sensitive T4 lysozyme mutant Arg 96 --> His.

Mooers, B.H.; Tronrud, D.E.; Matthews, B.W.

doi:10.2210/pdb3f8v/pdb

Macromolecule Content

Total Structure Weight: 19025.64
Atom Count: 1332
Residue Count: 164
Unique protein chains: 1

3F8V

Evaulaution at Atomic Resolution of the Role of Strain in Destabilizing the Temperature Sensitive T4 Lysozyme Mutant Arg96-->His

DOI: 10.2210/pdb3F8V/pdb

Classification: HYDROLASE
Organism(s): Enterobacteria phage T4
Expression System: Escherichia coli
Mutation(s): 1

Deposited: 2008-11-13 Released: 2009-02-17
Deposition Author(s): Mooers, B.H.M., Matthews, B.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.08 Å
R-Value Free: 0.163
R-Value Work: 0.129

wwPDB Validation3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Evaluation at atomic resolution of the role of strain in destabilizing the temperature-sensitive T4 lysozyme mutant Arg 96 --> His.

Mooers, B.H., Tronrud, D.E., Matthews, B.W.

(2009) Protein Sci. 18: 863-870

PubMed: 19384984 Search on PubMedSearch on PubMed Central
DOI: 10.1002/pro.93
Primary Citation of Related Structures:
3FAD, 3FA0, 3F9L
Also Cited By: 3FI5, 3CDV, 3CDT, 3CDR, 3CDQ, 3CDO, 3C8S, 3C8R, 3C8Q, 3C83, 3C82, 3C81, 3C80, 3C7Z, 3C7Y, 3C7W

PubMed Abstract:

Mutant R96H is a classic temperature-sensitive mutant of bacteriophage T4 lysozyme. It was in fact the first variant of the protein to be characterized structurally. Subsequently, it has been studied extensively by a variety of experimental and computational techniques, but the reasons for the loss of stability of the mutant protein remain controversial. In the crystallographic refinement of the mutant structure at 1.9 A resolution one of the bond angles at the site of substitution appeared to be distorted by about 11( degrees ), and it was suggested that this steric strain was one of the major factors in destabilizing the mutant. Different computationally-derived models of the mutant structure, however, did not show such distortion. To determine the geometry at the site of mutation more reliably, we have extended the resolution of the data and refined the wildtype (WT) and mutant structures to be better than 1.1 A resolution. The high-resolution refinement of the structure of R96H does not support the bond angle distortion seen in the 1.9 A structure determination. At the same time, it does confirm other manifestations of strain seen previously including an unusual rotameric state for His96 with distorted hydrogen bonding. The rotamer strain has been estimated as about 0.8 kcal/mol, which is about 25% of the overall reduction in stability of the mutant. Because of concern that contacts from a neighboring molecule in the crystal might influence the geometry at the site of mutation we also constructed and analyzed supplemental mutant structures in which this crystal contact was eliminated. High-resolution refinement shows that the crystal contacts have essentially no effect on the conformation of Arg96 in WT or on His96 in the R96H mutant.

Related Citations:

Contributions of all 20 amino acids at site 96 to the stability and structure of T4 lysozyme.
Mooers, B.H.,Baase, W.A.,Wray, J.W.,Matthews, B.W.
(2009) Protein Sci. 18: 871

Organizational Affiliation:

Howard Hughes Medical Institute, Institute of Molecular Biology and Department of Physics, 1229 University of Oregon Eugene, Oregon 97403-1229, USA.

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Lysozyme	A	164	Enterobacteria phage T4	Mutation(s): 1 Gene Names: E EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4) Go to UniProtKB: P00720
Protein Feature View Full Protein Feature View for P00720

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions	3D Interactions
K Query on K Download SDF File Download CCD File	A	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Ligand Interaction
PO4 Query on PO4 Download SDF File Download CCD File	A	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Ligand Interaction
NA Query on NA Download SDF File Download CCD File	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Ligand Interaction
CL Query on CL Download SDF File Download CCD File	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction
HED Query on HED Download SDF File Download CCD File	A	2-HYDROXYETHYL DISULFIDE C₄ H₁₀ O₂ S₂ KYNFOMQIXZUKRK-UHFFFAOYSA-N		Ligand Interaction