2PYK

Crystal structure of Staphylococcal nuclease variant V66Q/P117G/H124L/S128A at room temperature

Summary for 2PYK

• Entry DOI: 10.2210/pdb2pyk/pdb
• Related: 1U9R 2PW5 2PW7
• Descriptor: Thermonuclease (2 entities in total)
• Functional Keywords: staphylococcal nuclease, nuclease, hyperstable variant, internal waters, hydrolase
• Biological source: Staphylococcus aureus
• Cellular location: Secreted (By similarity): Q8NXI6
• Total number of polymer chains: 1
• Total formula weight: 16791.28

Authors

Schlessman, J.L.,Abe, C.,Garcia-Moreno, E.B. (deposition date: 2007-05-16, release date: 2008-05-20, Last modification date: 2024-04-03)

Primary citation

Schlessman, J.L.,Abe, C.,Gittis, A.,Karp, D.A.,Dolan, M.A.,Garcia-Moreno, E.B.
Crystallographic study of hydration of an internal cavity in engineered proteins with buried polar or ionizable groups.
Biophys.J., 94:3208-3216, 2008

PubMed Abstract: Although internal water molecules are essential for the structure and function of many proteins, the structural and physical factors that govern internal hydration are poorly understood. We have examined the molecular determinants of internal hydration systematically, by solving the crystal structures of variants of staphylococcal nuclease with Gln-66, Asn-66, and Tyr-66 at cryo (100 K) and room (298 K) temperatures, and comparing them with existing cryo and room temperature structures of variants with Glu-66, Asp-66, Lys-66, Glu-92 or Lys-92 obtained under conditions of pH where the internal ionizable groups are in the neutral state. At cryogenic temperatures the polar moieties of all these internal side chains are hydrated except in the cases of Lys-66 and Lys-92. At room temperature the internal water molecules were observed only in variants with Glu-66 and Tyr-66; water molecules in the other variants are probably present but they are disordered and therefore undetectable crystallographically. Each internal water molecule establishes between 3 and 5 hydrogen bonds with the protein or with other internal water molecules. The strength of interactions between internal polar side chains and water molecules seems to decrease from carboxylic acids to amides to amines. Low temperature, low cavity volume, and the presence of oxygen atoms in the cavity increase the positional stability of internal water molecules. This set of structures and the physical insight they contribute into internal hydration will be useful for the development and benchmarking of computational methods for artificial hydration of pockets, cavities, and active sites in proteins.

PubMed: 18178652
DOI: 10.1529/biophysj.107.122473

Experimental method

X-RAY DIFFRACTION (2.1 Å)