2PW5

Crystal Structure of Staphylococcal nuclease variant V66Y/P117G/H124L/S128A at room temperature

2PW5 の概要

• エントリーDOI: 10.2210/pdb2pw5/pdb
• 関連するPDBエントリー: 1U9R 2pw7
• 分子名称: Thermonuclease (2 entities in total)
• 機能のキーワード: staphyloccal nuclease, nuclease, hyperstable variant, internal waters, hydrolase
• 由来する生物種: Staphylococcus aureus
• 細胞内の位置: Secreted (By similarity): Q8NXI6
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 16826.32

構造登録者

Schlessman, J.L.,Abe, C.,Garcia-Moreno, E.B. (登録日: 2007-05-10, 公開日: 2008-04-22, 最終更新日: 2024-04-03)

主引用文献

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

実験手法

X-RAY DIFFRACTION (2.1 Å)