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Hydrolase (phosphoric diester) PDB id
1sty
Jmol
Contents
Protein chain
137 a.a. *
Ligands
THP
Metals
_CA
Waters ×147
* Residue conservation analysis
PDB id:
1sty
Name: Hydrolase (phosphoric diester)
Title: The alpha aneurism: a structural motif revealed in an insertion mutant of staphylococcal nuclease
Structure: Staphylococcal nuclease. Chain: a. Engineered: yes
Source: Staphylococcus aureus. Organism_taxid: 1280
Resolution:
1.67Å     R-factor:   0.170    
Authors: L.J.Keefe,E.E.Lattman
Key ref: L.J.Keefe et al. (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. PubMed id: 8475069 DOI: 10.1073/pnas.90.8.3275
Date:
18-Feb-93     Release date:   15-Apr-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

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

 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: 10.1073/pnas.90.8.3275 Proc Natl Acad Sci U S A 90:3275-3279 (1993)
PubMed id: 8475069  
 
 
The alpha aneurism: a structural motif revealed in an insertion mutant of staphylococcal nuclease.
L.J.Keefe, J.Sondek, D.Shortle, E.E.Lattman.
 
  ABSTRACT  
 
The x-ray crystal structure of a mutant of staphylococcal nuclease that contains a single glycine residue inserted in the C-terminal alpha-helix has been solved to 1.67 A resolution and refined to a crystallographic R value of 0.170. This inserted glycine residue is accommodated in the alpha-helix by formation of a previously uncharacterized bulge, which we term the alpha aneurism. A conformational search of known protein structures has identified the alpha aneurism in a number of protein families, including the histocompatibility antigens and hemoglobins.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21447339 M.Calixto-Gálvez, M.Romero-Díaz, A.García-Muñoz, A.Salas-Casas, J.Pais-Morales, I.J.Galván, E.Orozco, and M.A.Rodríguez (2011).
Identification of a polypeptide containing Tudor and staphyloccocal nuclease-like domains as the sequence-specific binding protein to the upstream regulatory element 1 of Entamoeba histolytica.
  Int J Parasitol, 41, 775-782.  
19217400 H.Tidow, A.Andreeva, T.J.Rutherford, and A.R.Fersht (2009).
Solution structure of the U11-48K CHHC zinc-finger domain that specifically binds the 5' splice site of U12-type introns.
  Structure, 17, 294-302.
PDB codes: 2vy4 2vy5
19357801 J.Devillé, J.Rey, and M.Chabbert (2009).
An indel in transmembrane helix 2 helps to trace the molecular evolution of class A G-protein-coupled receptors.
  J Mol Evol, 68, 475-489.  
16465590 L.Chakrabarti, J.T.Neal, M.Miles, R.A.Martinez, A.C.Smith, B.L.Sopher, and A.R.La Spada (2006).
The Purkinje cell degeneration 5J mutation is a single amino acid insertion that destabilizes Nna1 protein.
  Mamm Genome, 17, 103-110.  
15726624 M.Babor, H.M.Greenblatt, M.Edelman, and V.Sobolev (2005).
Flexibility of metal binding sites in proteins on a database scale.
  Proteins, 59, 221-230.  
16132464 S.Abe, P.L.Wang, F.Takahashi, and E.Sasaki (2005).
Structural analysis of cDNAs coding for 4SNc-Tudor domain protein from fish and their expression in yellowtail organs.
  Mar Biotechnol (NY), 7, 677-686.  
14645057 A.Caballero-Herrera, and L.Nilsson (2003).
Molecular dynamics simulations of the E1/E2 transmembrane domain of the Semliki Forest virus.
  Biophys J, 85, 3646-3658.  
10861938 D.M.Nguyen, A.G.Gittis, and E.E.Lattman (2000).
The duplication of an eight-residue helical stretch in Staphylococcal nuclease is not helical: a model for evolutionary change.
  Proteins, 40, 465-472.  
10966478 J.L.Popot, and D.M.Engelman (2000).
Helical membrane protein folding, stability, and evolution.
  Annu Rev Biochem, 69, 881-922.  
11025544 K.T.O'Neil, A.C.Bach, and W.F.DeGrado (2000).
Structural consequences of an amino acid deletion in the B1 domain of protein G.
  Proteins, 41, 323-333.  
  9739087 Y.Modis, S.A.Filppula, D.K.Novikov, B.Norledge, J.K.Hiltunen, and R.K.Wierenga (1998).
The crystal structure of dienoyl-CoA isomerase at 1.5 A resolution reveals the importance of aspartate and glutamate sidechains for catalysis.
  Structure, 6, 957-970.
PDB code: 1dci
9234995 N.Garnier, D.Genest, J.P.Duneau, and M.Genest (1997).
Molecular modeling of c-erbB2 receptor dimerization: coiled-coil structure of wild and oncogenic transmembrane domains--stabilization by interhelical hydrogen bonds in the oncogenic form.
  Biopolymers, 42, 157-168.  
  8976549 I.R.Vetter, W.A.Baase, D.W.Heinz, J.P.Xiong, S.Snow, and B.W.Matthews (1996).
Protein structural plasticity exemplified by insertion and deletion mutants in T4 lysozyme.
  Protein Sci, 5, 2399-2415.
PDB codes: 209l 210l 211l 212l 213l 214l 215l 218l 219l
8620531 P.Konig, R.Giraldo, L.Chapman, and D.Rhodes (1996).
The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA.
  Cell, 85, 125-136.
PDB code: 1ign
  7579648 D.Shortle, and J.Sondek (1995).
The emerging role of insertions and deletions in protein engineering.
  Curr Opin Biotechnol, 6, 387-393.  
8078936 A.A.Fedorov, K.A.Magnus, M.H.Graupe, E.E.Lattman, T.D.Pollard, and S.C.Almo (1994).
X-ray structures of isoforms of the actin-binding protein profilin that differ in their affinity for phosphatidylinositol phosphates.
  Proc Natl Acad Sci U S A, 91, 8636-8640.
PDB codes: 1acf 2acg
  7833814 I.L.Karle, J.L.Flippen-Anderson, R.Gurunath, and P.Balaram (1994).
Facile transition between 3(10)- and alpha-helix: structures of 8-, 9-, and 10-residue peptides containing the -(Leu-Aib-Ala)2-Phe-Aib- fragment.
  Protein Sci, 3, 1547-1555.  
  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
  7833813 P.Luginbühl, M.Ottiger, S.Mronga, and K.Wüthrich (1994).
Structure comparison of the pheromones Er-1, Er-10, and Er-2 from Euplotes raikovi.
  Protein Sci, 3, 1537-1546.  
  7920265 S.Bromberg, and K.A.Dill (1994).
Side-chain entropy and packing in proteins.
  Protein Sci, 3, 997.  
8290361 M.P.Laget, I.Callebaut, Y.de Launoit, D.Stehelin, and J.P.Mornon (1993).
Predicted common structural features of DNA-binding domains from Ets, Myb and HMG transcription factors.
  Nucleic Acids Res, 21, 5987-5996.  
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 codes are shown on the right.