3CDT

Contributions of all 20 amino acids at site 96 to the stability and structure of T4 lysozyme

Summary for 3CDT

• Entry DOI: 10.2210/pdb3cdt/pdb
• Related: 1L34 1L63 3C7W 3C7Y 3C7Z 3C80 3C81 3C82 3C83 3C8Q 3C8R 3C8S 3CDO 3CDQ 3CDR 3CDV 3F8V 3F9L 3FA0 3FAD 3FI5
• Descriptor: Lysozyme, CHLORIDE ION, BETA-MERCAPTOETHANOL, ... (4 entities in total)
• Functional Keywords: bacteriophage t4 lysozyme, viral lysozyme, mutational analysis, protein engineerng, thermal stability, protein stability, protein electrostatics, protein structure, cation binding, charge burial, hydrogen bonding, helix dipole, protein crevices, steric strain, temperature-sensitive mutant, antimicrobial, bacteriolytic enzyme, glycosidase, hydrolase
• Biological source: Bacteriophage T4 (VIRUS)
• Cellular location: Host cytoplasm : P00720
• Total number of polymer chains: 1
• Total formula weight: 18768.42

Authors

Mooers, B.H.M. (deposition date: 2008-02-27, release date: 2009-02-17, Last modification date: 2023-08-30)

Primary citation

Mooers, B.H.,Baase, W.A.,Wray, J.W.,Matthews, B.W.
Contributions of all 20 amino acids at site 96 to the stability and structure of T4 lysozyme.
Protein Sci., 18:871-880, 2009

PubMed Abstract: To try to resolve the loss of stability in the temperature-sensitive mutant of T4 lysozyme, Arg 96 --> His, all of the remaining 18 naturally occurring amino acids were substituted at site 96. Also, in response to suggestions that the charged residues Lys85 and Asp89, which are 5-8 A away, may have important effects, each of these amino acids was replaced with alanine. Crystal structures were determined for many of the variants. With the exception of the tryptophan and valine mutants R96W and R96V, the crystallographic analysis shows that the substituted side chain following the path of Arg96 in wildtype (WT). The melting temperatures of the variants decrease by up to approximately 16 degrees C with WT being most stable. There are two site 96 replacements, with lysine or glutamine, that leave the stability close to that of WT. The only element that the side chains of these residues have in common with the WT arginine is the set of three carbon atoms at the C(alpha), C(beta), and C(gamma) positions. Although each side chain is long and flexible with a polar group at the distal position, the details of the hydrogen bonding to the rest of the protein differ in each case. Also, the glutamine replacement lacks a positive charge. This shows that there is some adaptability in achieving full stabilization at this site. At the other extreme, to be maximally destabilizing a mutation at site 96 must not only eliminate favorable interactions but also introduce an unfavorable element such as steric strain or a hydrogen-bonding group that remains unsatisfied. Overall, the study highlights the essential need for atomic resolution site-specific structural information to understand and to predict the stability of mutant proteins. It can be very misleading to simply assume that conservative amino acid substitutions cause small changes in stability, whereas large stability changes are associated with nonconservative replacements.

PubMed: 19384988
DOI: 10.1002/pro.94

Experimental method

X-RAY DIFFRACTION (1.63 Å)