PDBsum entry 2pw7

Hydrolase

PDB id: 2pw7

Contents

Protein chain

130 a.a. *

Waters ×57

* Residue conservation analysis

PDB id:

2pw7

Name:

Hydrolase

Title:

Crystal structure of staphylococcal nuclease variant v66y/p117g/h124l/s128a at 100k

Structure:

Thermonuclease. Chain: a. Synonym: tnase, micrococcal nuclease, staphylococcal nuclease. Engineered: yes. Mutation: yes

Source:

Staphylococcus aureus. Organism_taxid: 1280. Gene: nuc. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.10Å R-factor: 0.223 R-free: 0.285

Authors:

J.L.Schlessman,C.Abe,E.B.Garcia-Moreno

Key ref:

J.L.Schlessman et al. (2008). Crystallographic study of hydration of an internal cavity in engineered proteins with buried polar or ionizable groups. Biophys J, 94, 3208-3216. PubMed id: 18178652

Date:

10-May-07 Release date: 22-Apr-08

Protein chain

A5A513  (A5A513_STAAU) -  Thermonuclease (Fragment) from Staphylococcus aureus

Seq: 215 a.a.

Struc: 130 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.3.1.31.1 - micrococcal nuclease.
• Reaction: Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotide end-products.

Biophys J 94:3208-3216 (2008)

PubMed id: 18178652

Crystallographic study of hydration of an internal cavity in engineered proteins with buried polar or ionizable groups.

J.L.Schlessman, C.Abe, A.Gittis, D.A.Karp, M.A.Dolan, B.García-Moreno E.

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.