PDBsum entry 2pzt

Go to PDB code: 
protein ligands links
Hydrolase PDB id
Jmol PyMol
Protein chain
130 a.a. *
Waters ×69
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Crystal structure of staphylococcal nuclease variant v66q/p117g/h124l/s128a at 100 k
Structure: Thermonuclease. Chain: a. Synonym: tnase, micrococcal nuclease, staphylococcal nuclease. Engineered: yes. Mutation: yes
Source: Staphylococcus aureus. Gene: nuc. Expressed in: escherichia coli.
2.10Å     R-factor:   0.207     R-free:   0.249
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
18-May-07     Release date:   20-May-08    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
A5A523  (A5A523_STAAU) -  Thermonuclease (Fragment)
215 a.a.
130 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Micrococcal nuclease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      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.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21389271 D.G.Isom, C.A.Castañeda, B.R.Cannon, and B.García-Moreno (2011).
Large shifts in pKa values of lysine residues buried inside a protein.
  Proc Natl Acad Sci U S A, 108, 5260-5265.  
20798341 D.G.Isom, C.A.Castañeda, B.R.Cannon, P.D.Velu, and B.García-Moreno E (2010).
Charges in the hydrophobic interior of proteins.
  Proc Natl Acad Sci U S A, 107, 16096-16100.  
21081092 M.A.Schroer, M.Paulus, C.Jeworrek, C.Krywka, S.Schmacke, Y.Zhai, D.C.Wieland, C.J.Sahle, M.Chimenti, C.A.Royer, B.Garcia-Moreno, M.Tolan, and R.Winter (2010).
High-pressure SAXS study of folded and unfolded ensembles of proteins.
  Biophys J, 99, 3430-3437.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.