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Hydrolase(phosphoric diester) PDB id
1stn
Jmol
Contents
Protein chain
136 a.a. *
Waters ×83
* Residue conservation analysis
PDB id:
1stn
Name: Hydrolase(phosphoric diester)
Title: The crystal structure of staphylococcal nuclease refined at 1.7 angstroms resolution
Structure: Staphylococcal nuclease. Chain: a. Engineered: yes
Source: Staphylococcus aureus. Organism_taxid: 1280
Resolution:
1.70Å     R-factor:   0.162    
Authors: T.R.Hynes,R.O.Fox
Key ref: T.R.Hynes and R.O.Fox (1991). The crystal structure of staphylococcal nuclease refined at 1.7 A resolution. Proteins, 10, 92. PubMed id: 1896431 DOI: 10.1002/prot.340100203
Date:
17-Feb-93     Release date:   31-Jul-94    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00644  (NUC_STAAU) -  Thermonuclease
Seq:
Struc: 		231 a.a.
136 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.31.1  - 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/prot.340100203 Proteins 10:92 (1991)
PubMed id: 1896431  
 
 
The crystal structure of staphylococcal nuclease refined at 1.7 A resolution.
T.R.Hynes, R.O.Fox.
 
  ABSTRACT  
 
The crystal structure of staphylococcal nuclease has been determined to 1.7 A resolution with a final R-factor of 16.2% using stereochemically restrained Hendrickson-Konnert least-squares refinement. The structure reveals a number of conformational changes relative to the structure of the ternary complex of staphylococcal nuclease 1,2 bound with deoxythymidine-3',5'-diphosphate and Ca2+. Tyr-113 and Tyr-115, which pack against the nucleotide base in the nuclease complex, are rotated outward creating a more open binding pocket in the absence of nucleotide. The side chains of Ca2+ ligands Asp-21 and Asp-40 shift as does Glu-43, the proposed general base in the hydrolysis of the 5'-phosphodiester bond. The significance of some changes in the catalytic site is uncertain due to the intrusion of a symmetry related Lys-70 side chain which hydrogen bonds to both Asp-21 and Glu-43. The position of a flexible loop centered around residue 50 is altered, most likely due to conformational changes propagated from the Ca2+ site. The side chains of Arg-35, Lys-84, Tyr-85, and Arg-87, which hydrogen bond to the 3'- and 5'-phosphates of the nucleotide in the nuclease complex, are unchanged in conformation, with packing interactions with adjacent protein side chains sufficient to fix the geometry in the absence of ligand. The nuclease structure presented here, in combination with the stereochemically restrained refinement of the nuclease complex structure at 1.65 A, provides a wealth of structural information for the increasing number of studies using staphylococcal nuclease as a model system of protein structure and function.
 

Literature references that cite this PDB file's key reference

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PDB code: 1u9r
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PDB codes: 1eif 2eif
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PDB codes: 2tss 3tss 4tss 5tss
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Three-dimensional diffuse x-ray scattering from crystals of Staphylococcal nuclease.
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Predicting the equilibrium protein folding pathway: structure-based analysis of staphylococcal nuclease.
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Molecular characterization of a major serotype M49 group A streptococcal DNase gene (sdaD).
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A fragment of staphylococcal nuclease with an OB-fold structure shows hydrogen-exchange protection factors in the range reported for "molten globules".
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PDB codes: 1sno 1snp 1snq
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Yeast heat shock transcription factor N-terminal activation domains are unstructured as probed by heteronuclear NMR spectroscopy.
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Crystal structure of an ATP-dependent DNA ligase from bacteriophage T7.
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PDB code: 1a0i
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Mapping the structure of a non-native state of staphylococcal nuclease.
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Mobile unnatural amino acid side chains in the core of staphylococcal nuclease.
  Protein Sci, 5, 1026-1031.
PDB codes: 1a2t 1a2u 1aex 1nuc 2nuc 3nuc 5nuc
  7613463 A.Hodel, L.M.Rice, T.Simonson, R.O.Fox, and A.T.Brünger (1995).
Proline cis-trans isomerization in staphylococcal nuclease: multi-substrate free energy perturbation calculations.
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  7795531 A.Hodel, R.A.Kautz, and R.O.Fox (1995).
Stabilization of a strained protein loop conformation through protein engineering.
  Protein Sci, 4, 484-495.
PDB codes: 1kda 1kdb 1kdc
7582973 J.Light, and R.A.Lerner (1995).
Random mutagenesis of staphylococcal nuclease and phage display selection.
  Bioorg Med Chem, 3, 955-967.  
7476164 K.Schröder, P.Graumann, A.Schnuchel, T.A.Holak, and M.A.Marahiel (1995).
Mutational analysis of the putative nucleic acid-binding surface of the cold-shock domain, CspB, revealed an essential role of aromatic and basic residues in binding of single-stranded DNA containing the Y-box motif.
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7664121 L.Mosyak, L.Reshetnikova, Y.Goldgur, M.Delarue, and M.G.Safro (1995).
Structure of phenylalanyl-tRNA synthetase from Thermus thermophilus.
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PDB code: 1pys
  8528079 R.Wynn, C.L.Anderson, F.M.Richards, and R.O.Fox (1995).
Interactions in nonnative and truncated forms of staphylococcal nuclease as indicated by mutational free energy changes.
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  7735833 S.Onesti, A.D.Miller, and P.Brick (1995).
The crystal structure of the lysyl-tRNA synthetase (LysU) from Escherichia coli.
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PDB code: 1lyl
8031301 A.P.Wolffe (1994).
Structural and functional properties of the evolutionarily ancient Y-box family of nucleic acid binding proteins.
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8197194 H.Schindelin, W.Jiang, M.Inouye, and U.Heinemann (1994).
Crystal structure of CspA, the major cold shock protein of Escherichia coli.
  Proc Natl Acad Sci U S A, 91, 5119-5123.
PDB code: 1mjc
  8019410 L.J.Keefe, S.Quirk, A.Gittis, J.Sondek, and E.E.Lattman (1994).
Accommodation of insertion mutations on the surface and in the interior of staphylococcal nuclease.
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PDB codes: 1sta 1stb
8290547 M.D.Jacobs, and R.O.Fox (1994).
Staphylococcal nuclease folding intermediate characterized by hydrogen exchange and NMR spectroscopy.
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OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences.
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Stress and strain in staphylococcal nuclease.
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PDB codes: 1kaa 1kab
  8495202 R.A.Kautz, and R.O.Fox (1993).
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8234243 W.J.Chuang, D.J.Weber, A.G.Gittis, and A.S.Mildvan (1993).
Mutational tests of the NMR-docked structure of the staphylococcal nuclease-metal-3',5'-pdTp complex.
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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. Where a reference describes a PDB structure, the PDB code is shown on the right.