PDBsum entry 1aex

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Nuclease PDB id
Protein chain
135 a.a. *
Waters ×96
* Residue conservation analysis
PDB id:
Name: Nuclease
Title: Staphylococcal nuclease, methane thiol disulfide to v23c variant
Structure: Staphylococcal nuclease. Chain: a. Engineered: yes. Mutation: yes. Other_details: pdtp, 3',5'-thymidine diphosphate, methane thiol disulfide
Source: Staphylococcus aureus. Organism_taxid: 1280. Expressed in: escherichia coli. Expression_system_taxid: 562.
2.10Å     R-factor:   0.181    
Authors: R.Wynn,P.C.Harkins,F.M.Richards,R.O.Fox
Key ref: R.Wynn et al. (1996). Mobile unnatural amino acid side chains in the core of staphylococcal nuclease. Protein Sci, 5, 1026-1031. PubMed id: 8762134 DOI: 10.1002/pro.5560050605
01-Mar-97     Release date:   16-Jun-97    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P00644  (NUC_STAAU) -  Thermonuclease
231 a.a.
135 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.  - Micrococcal nuclease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotide end-products.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     nucleic acid binding     3 terms  


DOI no: 10.1002/pro.5560050605 Protein Sci 5:1026-1031 (1996)
PubMed id: 8762134  
Mobile unnatural amino acid side chains in the core of staphylococcal nuclease.
R.Wynn, P.C.Harkins, F.M.Richards, R.O.Fox.
The structures of several variants of staphylococcal nuclease with long flexible unnatural amino acid side chains in the hydrophobic core have been determined by X-ray crystallography. The unnatural amino acids are disulfide moieties between the lone cysteine residue in V23C nuclease and methane, ethane, 1-n-propane, 1-n-butane, 1-n-pentane, and 2-hydroxyethyl thiols. We have examined changes in the core packing of these mutants. Side chains as large as the 1-n-propyl cysteine disulfide can be incorporated without perturbation of the structure. This is due, in part, to cavities present in the wild-type protein. The longest side chains are not well defined, even though they remain buried within the protein interior. These results suggest that the enthalpy-entropy balance that governs the rigidity of protein interiors favors tight packing only weakly. Additionally, the tight packing observed normally in protein interiors may reflect, in part, the limited numbers of rotamers available to the natural amino acids.

Literature references that cite this PDB file's key reference

  PubMed id Reference
17473014 Z.Guo, D.Cascio, K.Hideg, T.Kálái, and W.L.Hubbell (2007).
Structural determinants of nitroxide motion in spin-labeled proteins: tertiary contact and solvent-inaccessible sites in helix G of T4 lysozyme.
  Protein Sci, 16, 1069-1086.
PDB codes: 2igc 2ntg 2nth 2ou8 2ou9
15260581 J.Zhang, Y.Chen, R.Chen, and J.Liang (2004).
Importance of chirality and reduced flexibility of protein side chains: a study with square and tetrahedral lattice models.
  J Chem Phys, 121, 592-603.  
9558332 G.DeSantis, P.Berglund, M.R.Stabile, M.Gold, and J.B.Jones (1998).
Site-directed mutagenesis combined with chemical modification as a strategy for altering the specificity of the S1 and S1' pockets of subtilisin Bacillus lentus.
  Biochemistry, 37, 5968-5973.  
  9792110 K.J.Frye, and C.A.Royer (1998).
Probing the contribution of internal cavities to the volume change of protein unfolding under pressure.
  Protein Sci, 7, 2217-2222.  
  9336831 G.Raghunathan, and R.L.Jernigan (1997).
Ideal architecture of residue packing and its observation in protein structures.
  Protein Sci, 6, 2072-2083.  
  9194193 R.O'Brien, R.Wynn, P.C.Driscoll, B.Davis, K.W.Plaxco, J.M.Sturtevant, and J.E.Ladbury (1997).
The adaptability of Escherichia coli thioredoxin to non-conservative amino acid substitutions.
  Protein Sci, 6, 1325-1332.  
  9260275 R.Wynn, P.C.Harkins, F.M.Richards, and R.O.Fox (1997).
Comparison of straight chain and cyclic unnatural amino acids embedded in the core of staphylococcal nuclease.
  Protein Sci, 6, 1621-1626.
PDB codes: 1a3t 1a3u 1a3v
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