Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18871.54 
• Atom Count: 1303 
• Residue Count: 164 
• Unique protein chains: 1

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

• DOI: 10.2210/pdb120L/pdb

• Classification: HYDROLASE(O-GLYCOSYL)
• Organism(s): Enterobacteria phage T4


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å

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 
• Primary Citation of Related Structures:  
  224L, 221L, 206L, 128L, 127L, 126L, 125L, 123L, 122L, 119L, 118L


• 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.

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Related Citations: 

• Structure of Bacteriophage T4 Lysozyme Refined at 1.7 Angstroms Resolution
  Weaver, L.H.,Matthews, B.W.
  (1987) J.Mol.Biol. 193: 189
• Control of Enzyme Activity by an Engineered Disulfide Bond
  Matsumura, M.,Matthews, B.W.
  (1989) Science 243: 792




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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
T4 LYSOZYME	A	164	Enterobacteria phage T4	Gene Names: E EC: 3.2.1.17
Find proteins for P00720 (Enterobacteria phage T4) Go to UniProtKB:  P00720

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
BME	A	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• Space Group: P 3₂ 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 61.300	α = 90.00
b = 61.300	β = 90.00
c = 97.200	γ = 120.00

Software Package:

Software Name	Purpose
TNT	refinement

Structure Validation

Entry History 

Deposition Data

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

Revision History 

• Version 1.0: 1993-10-31
  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