PDBsum entry 1ena

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Hydrolase(phosphoric diester) PDB id
Protein chain
135 a.a. *
Waters ×34
* Residue conservation analysis
PDB id:
Name: Hydrolase(phosphoric diester)
Title: Crystal structures of the binary ca2+ and pdtp complexes and the ternary complex of the asp 21->glu mutant of staphylococcal nuclease. Implications for catalysis and ligand binding
Structure: Staphylococcal nuclease. Chain: a. Engineered: yes
Source: Staphylococcus aureus. Organism_taxid: 1280
2.15Å     R-factor:   0.225    
Authors: A.Libson,A.Gittis,E.E.Lattman
Key ref:
A.M.Libson et al. (1994). Crystal structures of the binary Ca2+ and pdTp complexes and the ternary complex of the Asp21-->Glu mutant of staphylococcal nuclease. Implications for catalysis and ligand binding. Biochemistry, 33, 8007-8016. PubMed id: 8025105 DOI: 10.1021/bi00192a004
14-Feb-94     Release date:   31-May-94    
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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: 10.1021/bi00192a004 Biochemistry 33:8007-8016 (1994)
PubMed id: 8025105  
Crystal structures of the binary Ca2+ and pdTp complexes and the ternary complex of the Asp21-->Glu mutant of staphylococcal nuclease. Implications for catalysis and ligand binding.
A.M.Libson, A.G.Gittis, E.E.Lattman.
The crystal structure of the Asp21-->Glu mutant (D21E) of staphylococcal nuclease (SNase) has been determined in three different complex forms. The structure of the D21E ternary complex in which D21E is bound to both Ca2+ and the transition-state analogue, thymidine 3',5'-diphosphate (pdTp), was determined to 1.95-A resolution. The structures of both binary complexes, D21E bound either to Ca2+ or pdTp, were determined to 2.15- and 2.05-A resolution, respectively. In the ternary structure, we find a 1.5-A movement of the Ca2+ in the active site, evidence of bidentate coordination of Ca2+ by Glu21 and inner-sphere coordination of the Ca2+ by Glu43. Comparison of the D21E binary structures with the ternary model shows large movements of active site side chains expected to play a direct role in catalysis. Glu43 moves in the binary nucleotide complex, whereas Arg35 is oriented differently in the binary metal complex. From these changes, we seek to explain the basis for the 1500-fold decrease in Vmax of D21E relative to wild-type SNase (WT). Furthermore, we describe direct structural evidence which explains the cooperativity of Ca2+ and pdTp binding in the ternary complex relative to that of the binary complexes.

Literature references that cite this PDB file's key reference

  PubMed id Reference
18453631 C.L.Li, W.Z.Yang, Y.P.Chen, and H.S.Yuan (2008).
Structural and functional insights into human Tudor-SN, a key component linking RNA interference and editing.
  Nucleic Acids Res, 36, 3579-3589.
PDB code: 3bdl
11742693 E.S.Rangarajan, and V.Shankar (2001).
Sugar non-specific endonucleases.
  FEMS Microbiol Rev, 25, 583-613.  
10913261 B.Sundararaju, H.Chen, S.Shilcutt, and R.S.Phillips (2000).
The role of glutamic acid-69 in the activation of Citrobacter freundii tyrosine phenol-lyase by monovalent cations.
  Biochemistry, 39, 8546-8555.  
10329653 J.J.Steenhuis, R.S.Hutchison, and B.A.Barry (1999).
Alterations in carboxylate ligation at the active site of photosystem II.
  J Biol Chem, 274, 14609-14616.  
  9041650 C.P.Ponting (1997).
P100, a transcriptional coactivator, is a human homologue of staphylococcal nuclease.
  Protein Sci, 6, 459-463.  
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.