120L

THE ENERGETIC COST AND THE STRUCTURAL CONSEQUENCES OF BURYING A HYDROXYL GROUP WITHIN THE CORE OF A PROTEIN DETERMINED FROM ALA TO SER AND VAL TO THR SUBSTITUTIONS IN T4 LYSOZYME

PDB DOI: 10.2210/pdb120L/pdb

Classification: HYDROLASE(O-GLYCOSYL)
Organism(s): Escherichia virus T4
Mutation(s): No

Deposited: 1993-05-28 Released: 1993-10-31
Deposition Author(s): Blaber, M., Matthews, B.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Observed: 0.162

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Energetic cost and structural consequences of burying a hydroxyl group within the core of a protein determined from Ala-->Ser and Val-->Thr substitutions in T4 lysozyme.

Blaber, M., Lindstrom, J.D., Gassner, N., Xu, J., Heinz, D.W., Matthews, B.W.

(1993) Biochemistry 32: 11363-11373

PubMed: 8218201 Search on PubMed
DOI: 10.1021/bi00093a013
Primary Citation of Related Structures:
118L, 119L, 120L, 122L, 123L, 125L, 126L, 127L, 128L, 206L, 221L, 224L

PubMed Abstract:

In order to determine the thermodynamic cost of introducing a polar group within the core of a protein, a series of nine Ala-->Ser and 3 Val-->Thr substitutions was constructed in T4 lysozyme. The sites were all within alpha-helices but ranged from fully solvent-exposed to totally buried. The range of destabilization incurred by the Ala-->Ser substitutions was found to be very similar to that for the Val-->Thr replacements. For the solvent-exposed and partly exposed sites the destabilization was modest (approximately less than 0.5 kcal/mol). For the completely buried sites the destabilization was larger, but variable (approximately 1-3 kcal/mol). Crystal structure determinations showed that the Ala-->Ser mutant structures were, in general, very similar to their wild-type counterparts, even though the replacements introduce a hydroxyl group. This is in part because the introduced serines are all within alpha-helices and at congested sites can avoid steric clashes with surrounding atoms by making a hydrogen bond to a backbone carbonyl oxygen in the preceding turn of the helix. The three substituted threonine side chains essentially superimpose on their valine counterparts but display somewhat larger conformational adjustments. The results illustrate how a protein structure will adapt in different ways to avoid the presence of an unsatisfied hydrogen bond donor or acceptor. In the most extreme case, Val 149-->Thr, which is also the most destabilizing variant (delta delta G = 2.8 kcal/mol), a water molecule is incorporated in the mutant structure in order to provide a hydrogen-bonding partner. The results are consistent with the view that many hydrogen bonds within proteins contribute only marginally to stability but that noncharged polar groups that lack a hydrogen-bonding partner are very destabilizing (delta delta G approximately greater than 3 kcal/mol). Supportive of other studies, the alpha-helix propensity of alanine is seen to be higher than that of serine (delta delta G = 0.46 +/- 0.04 kcal/mol), while threonine and valine are similar in alpha-helix propensity.

Related Citations:

Control of Enzyme Activity by an Engineered Disulfide Bond
Matsumura, M., Matthews, B.W.
(1989) Science 243: 792

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, Eugene, Oregon.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T4 LYSOZYME	A	164	Escherichia virus T4	Mutation(s): 0 Gene Names: E EC: 3.2.1.17
UniProt
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720 Go to UniProtKB: P00720
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P00720
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BME Query on BME Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A]	D [auth A], E [auth A]	BETA-MERCAPTOETHANOL C₂ H₆ O S DGVVWUTYPXICAM-UHFFFAOYSA-N		Ligand Interaction
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A]	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Ligand Interaction