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Hydrolase (phosphoric diester) PDB id
1snc
Jmol
Contents
Protein chain
135 a.a. *
Ligands
THP
Metals
_CA
Waters ×82
* Residue conservation analysis
PDB id:
1snc
Name: Hydrolase (phosphoric diester)
Title: The crystal structure of the ternary complex of staphylococcal nuclease, ca2+, and the inhibitor pd Tp, refined at 1.65 angstroms
Structure: Thermonuclease precursor. Chain: a. Engineered: yes
Source: Staphylococcus aureus. Organism_taxid: 1280
Resolution:
1.65Å     R-factor:   0.161    
Authors: P.J.Loll,E.E.Lattman
Key ref: P.J.Loll and E.E.Lattman (1989). The crystal structure of the ternary complex of staphylococcal nuclease, Ca2+, and the inhibitor pdTp, refined at 1.65 A. Proteins, 5, 183-201. PubMed id: 2780539 DOI: 10.1002/prot.340050302
Date:
21-Jul-89     Release date:   15-Oct-90    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00644  (NUC_STAAU) -  Thermonuclease
Seq:
Struc: 		231 a.a.
135 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.340050302 Proteins 5:183-201 (1989)
PubMed id: 2780539  
 
 
The crystal structure of the ternary complex of staphylococcal nuclease, Ca2+, and the inhibitor pdTp, refined at 1.65 A.
P.J.Loll, E.E.Lattman.
 
  ABSTRACT  
 
The structure of a complex of staphylococcal nuclease with Ca2+ and deoxythymidine 3',5'-bisphosphate (pdTp) has been refined by stereochemically restrained least-squares minimization to a crystallographic R value of 0.161 at 1.65 A resolution. The estimated root-mean-square (rms) error in the coordinates is 0.16 A. The final model comprises 1082 protein atoms, one calcium ion, the pdTp molecule, and 82 solvent water molecules; it displays an rms deviation from ideality of 0.017 A for bond distances and 1.8 degrees for bond angles. The mean distance between corresponding alpha carbons in the refined and unrefined structures is 0.6 A; we observe small but significant differences between the refined and unrefined models in the turn between residues 27 and 30, the loop between residues 44 and 50, the first helix, and the extended strand between residues 112 and 117 which forms part of the active site binding pocket. The details of the calcium liganding and solvent structure in the active site are clearly shown in the final electron density map. The structure of the catalytic site is consistent with the mechanism that has been proposed for this enzyme. However, we note that two lysines from a symmetry-related molecule in the crystal lattice may play an important role in determining the geometry of inhibitor binding, and that only one of the two required calcium ions is observed in the crystal structure; thus, caution is advised in extrapolating from the structure of the complex of enzyme and inhibitor to that of enzyme and substrate.
 

Literature references that cite this PDB file's key reference

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PDB code: 2rks
18260114 M.Onitsuka, H.Kamikubo, Y.Yamazaki, and M.Kataoka (2008).
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12021428 Y.Liu, and D.Eisenberg (2002).
3D domain swapping: as domains continue to swap.
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11488916 F.Yang, Y.Cheng, J.Peng, J.Zhou, and G.Jing (2001).
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11598114 K.W.Leung, Y.C.Liaw, S.C.Chan, H.Y.Lo, F.N.Musayev, J.Z.Chen, H.J.Fang, and H.M.Chen (2001).
Significance of local electrostatic interactions in staphylococcal nuclease studied by site-directed mutagenesis.
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10861938 D.M.Nguyen, A.G.Gittis, and E.E.Lattman (2000).
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10656260 J.O.Wrabl, D.Shortle, and T.B.Woolf (2000).
Correlation between changes in nuclear magnetic resonance order parameters and conformational entropy: molecular dynamics simulations of native and denatured staphylococcal nuclease.
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  9514257 R.Aurora, and G.D.Rose (1998).
Helix capping.
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Identification of cooperative folding units in a set of native proteins.
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P100, a transcriptional coactivator, is a human homologue of staphylococcal nuclease.
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9038220 D.Wang, and R.Landick (1997).
Nuclease cleavage of the upstream half of the nontemplate strand DNA in an Escherichia coli transcription elongation complex causes upstream translocation and transcriptional arrest.
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Identification of compact, hydrophobically stabilized domains and modules containing multiple peptide chains.
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Comparison of straight chain and cyclic unnatural amino acids embedded in the core of staphylococcal nuclease.
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PDB codes: 1a3t 1a3u 1a3v
9061781 V.J.Hilser, and E.Freire (1997).
Predicting the equilibrium protein folding pathway: structure-based analysis of staphylococcal nuclease.
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Coupling between trans/cis proline isomerization and protein stability in staphylococcal nuclease.
  Protein Sci, 5, 1907-1916.
PDB codes: 1sno 1snp 1snq
8924198 M.P.Byrne, C.A.Broomfield, and W.E.Stites (1996).
Mustard gas crosslinking of proteins through preferential alkylation of cysteines.
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Mobile unnatural amino acid side chains in the core of staphylococcal nuclease.
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PDB codes: 1a2t 1a2u 1aex 1nuc 2nuc 3nuc 5nuc
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Proline cis-trans isomerization in staphylococcal nuclease: multi-substrate free energy perturbation calculations.
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PDB codes: 1kda 1kdb 1kdc
8789192 C.S.Poornima, and P.M.Dean (1995).
Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions.
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8789193 C.S.Poornima, and P.M.Dean (1995).
Hydration in drug design. 2. Influence of local site surface shape on water binding.
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7582973 J.Light, and R.A.Lerner (1995).
Random mutagenesis of staphylococcal nuclease and phage display selection.
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  7587280 K.C.Chou, and C.T.Zhang (1995).
Prediction of protein structural classes.
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7782335 M.Iyer, J.C.Norton, and D.R.Corey (1995).
Accelerated hybridization of oligonucleotides to duplex DNA.
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3D domain swapping: a mechanism for oligomer assembly.
  Protein Sci, 4, 2455-2468.  
8592698 N.N.Kalnin, and K.Kuwajima (1995).
Kinetic folding and unfolding of staphylococcal nuclease and its six mutants studied by stopped-flow circular dichroism.
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The importance of anchorage in determining a strained protein loop conformation.
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Thermodynamics of staphylococcal nuclease denaturation. I. The acid-denatured state.
  Protein Sci, 3, 944-951.  
  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.
  Protein Sci, 3, 391-401.
PDB codes: 1sta 1stb
8290547 M.D.Jacobs, and R.O.Fox (1994).
Staphylococcal nuclease folding intermediate characterized by hydrogen exchange and NMR spectroscopy.
  Proc Natl Acad Sci U S A, 91, 449-453.  
8146123 W.J.Chuang, A.G.Gittis, and A.S.Mildvan (1994).
Magnetic resonance studies of the binding of oligonucleotide substrates to mutants of staphylococcal nuclease.
  Proteins, 18, 68-80.  
  8458342 A.G.Murzin (1993).
OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences.
  EMBO J, 12, 861-867.  
  8495201 A.Hodel, R.A.Kautz, M.D.Jacobs, and R.O.Fox (1993).
Stress and strain in staphylococcal nuclease.
  Protein Sci, 2, 838-850.
PDB codes: 1kaa 1kab
  8069624 C.A.Orengo, and J.M.Thornton (1993).
Alpha plus beta folds revisited: some favoured motifs.
  Structure, 1, 105-120.  
8234242 D.J.Weber, E.H.Serpersu, A.G.Gittis, E.E.Lattman, and A.S.Mildvan (1993).
NMR docking of the competitive inhibitor thymidine 3',5'-diphosphate into the X-ray structure of staphylococcal nuclease.
  Proteins, 17, 20-35.  
8475069 L.J.Keefe, J.Sondek, D.Shortle, and E.E.Lattman (1993).
The alpha aneurism: a structural motif revealed in an insertion mutant of staphylococcal nuclease.
  Proc Natl Acad Sci U S A, 90, 3275-3279.
PDB code: 1sty
8394001 M.H.Zehfus (1993).
Improved calculations of compactness and a reevaluation of continuous compact units.
  Proteins, 16, 293-300.  
  8495202 R.A.Kautz, and R.O.Fox (1993).
NMR analysis of staphylococcal nuclease thermal quench refolding kinetics.
  Protein Sci, 2, 851-858.  
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.
  Proteins, 17, 36-48.  
1511238 G.W.Vuister, and A.Bax (1992).
Measurement of two-bond JCOH alpha coupling constants in proteins uniformly enriched with 13C.
  J Biomol NMR, 2, 401-405.  
1731350 J.M.Flanagan, M.Kataoka, D.Shortle, and D.M.Engelman (1992).
Truncated staphylococcal nuclease is compact but disordered.
  Proc Natl Acad Sci U S A, 89, 748-752.  
1620695 J.Sondek, and D.Shortle (1992).
Structural and energetic differences between insertions and substitutions in staphylococcal nuclease.
  Proteins, 13, 132-140.  
1511237 Y.Liu, D.Zhao, R.Altman, and O.Jardetzky (1992).
A systematic comparison of three structure determination methods from NMR data: dependence upon quality and quantity of data.
  J Biomol NMR, 2, 373-388.  
  1721649 D.C.Benjamin (1991).
Molecular approaches to the study of B cell epitopes.
  Int Rev Immunol, 7, 149-164.  
1841710 F.Delaglio, D.A.Torchia, and A.Bax (1991).
Measurement of 15N-13C J couplings in staphylococcal nuclease.
  J Biomol NMR, 1, 439-446.  
1896431 T.R.Hynes, and R.O.Fox (1991).
The crystal structure of staphylococcal nuclease refined at 1.7 A resolution.
  Proteins, 10, 92.
PDB code: 1stn
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