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PDBsum entry 1de3

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protein links
Hydrolase PDB id
1de3
Jmol
Contents
Protein chain
150 a.a. *
* Residue conservation analysis
PDB id:
1de3
Name: Hydrolase
Title: Solution structure of the cytotoxic ribonuclease alpha- sarcin
Structure: Ribonuclease alpha-sarcin. Chain: a. Engineered: yes
Source: Aspergillus giganteus. Organism_taxid: 5060. Strain: mdh 18894. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 20 models
Authors: J.M.Perez-Canadillas,R.Campos-Olivas,J.Santoro,J.Lacadena, A.Martinez Del Pozo,J.G.Gavilanes,M.Rico,M.Bruix
Key ref:
J.M.Pérez-Cañadillas et al. (2000). The highly refined solution structure of the cytotoxic ribonuclease alpha-sarcin reveals the structural requirements for substrate recognition and ribonucleolytic activity. J Mol Biol, 299, 1061-1073. PubMed id: 10843858 DOI: 10.1006/jmbi.2000.3813
Date:
12-Nov-99     Release date:   21-Jun-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00655  (RNAS_ASPGI) -  Ribonuclease alpha-sarcin
Seq:
Struc:
177 a.a.
150 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.1.27.10  - rRNA endonuclease.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of the phosphodiester linkage between guanosine and adenosine residues at one specific position in the 28S rRNA from rat ribosomes.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   1 term 
  Biological process     metabolic process   5 terms 
  Biochemical function     hydrolase activity     6 terms  

 

 
DOI no: 10.1006/jmbi.2000.3813 J Mol Biol 299:1061-1073 (2000)
PubMed id: 10843858  
 
 
The highly refined solution structure of the cytotoxic ribonuclease alpha-sarcin reveals the structural requirements for substrate recognition and ribonucleolytic activity.
J.M.Pérez-Cañadillas, J.Santoro, R.Campos-Olivas, J.Lacadena, A.Martínez del Pozo, J.G.Gavilanes, M.Rico, M.Bruix.
 
  ABSTRACT  
 
alpha-Sarcin selectively cleaves a single phosphodiester bond in a universally conserved sequence of the major rRNA, that inactivates the ribosome. The elucidation of the three-dimensional solution structure of this 150 residue enzyme is a crucial step towards understanding alpha-sarcin's conformational stability, ribonucleolytic activity, and its exceptionally high level of specificity. Here, the solution structure has been determined on the basis of 2658 conformationally relevant distances restraints (including stereoespecific assignments) and 119 torsional angular restraints, by nuclear magnetic resonance spectroscopy methods. A total of 60 converged structures have been computed using the program DYANA. The 47 best DYANA structures, following restrained energy minimization by GROMOS, represent the solution structure of alpha-sarcin. The resulting average pairwise root-mean-square-deviation is 0.86 A for backbone atoms and 1.47 A for all heavy atoms. When the more variable regions are excluded from the analysis, the pairwise root-mean-square deviation drops to 0.50 A and 1.00 A, for backbone and heavy atoms, respectively. The alpha-sarcin structure is similar to that reported for restrictocin, although some differences are clearly evident, especially in the loop regions. The average rmsd between the structurally aligned backbones of the 47 final alpha-sarcin structures and the crystal structure of restrictocin is 1.46 A. On the basis of a docking model constructed with alpha-sarcin solution structure and the crystal structure of a 29-nt RNA containing the sarcin/ricin domain, the regions in the protein that could interact specifically with the substrate have been identified. The structural elements that account for the specificity of RNA recognition are located in two separate regions of the protein. One is composed by residues 51 to 55 and loop 5, and the other region, located more than 11 A away in the structure, is the positively charged segment formed by residues 110 to 114.
 
  Selected figure(s)  
 
Figure 5.
Figure 5. Structural comp arison of a-sarcin and restrictocin. (a) Superposition of the lowest energy solution structure of a-sarcin (black, residues 1 to 150) and the crystal structure of restrictocin (RCSB PDB entry 1AQZ, chain A) (gray, residues 1 to 10, 17 to 149). (b) Detail of the superposition of the N-terminal hairpin; the discontinuity in the crystal structure of restrictocin is due to the lack of electron density for residues 11 to 16. (c) Superposition of loop 2 where the largest differences are found.
Figure 6.
Figure 6. Model of the interaction between the 28S rat SRD (Sarcin Ricin Domain) and a-sarcin. The protein is represented by the electrostatic surface and the RNA fragment with a stick model. The phosphodiester chain is colored in red, the recognition guanine G4310 in green and the bases adjacent to the scissile bond, A4324 and G4325, in yellow. Recognition sites and the N-terminal hairpin in the protein structure are labeled. Figure generated with GRASP.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2000, 299, 1061-1073) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20843477 E.F.Fang, and T.B.Ng (2011).
Ribonucleases of different origins with a wide spectrum of medicinal applications.
  Biochim Biophys Acta, 1815, 65-74.  
20375171 I.S.Kim, S.D.Trask, M.Babyonyshev, P.R.Dormitzer, and S.C.Harrison (2010).
Effect of mutations in VP5 hydrophobic loops on rotavirus cell entry.
  J Virol, 84, 6200-6207.  
20215430 L.García-Ortega, E.Alvarez-García, J.G.Gavilanes, A.Martínez-del-Pozo, and S.Joseph (2010).
Cleavage of the sarcin-ricin loop of 23S rRNA differentially affects EF-G and EF-Tu binding.
  Nucleic Acids Res, 38, 4108-4119.  
19348010 A.Viegas, E.Herrero-Galán, M.Oñaderra, A.L.Macedo, and M.Bruix (2009).
Solution structure of hirsutellin A--new insights into the active site and interacting interfaces of ribotoxins.
  FEBS J, 276, 2381-2390.
PDB code: 2kaa
18214983 E.Herrero-Galán, J.Lacadena, A.Martínez del Pozo, D.G.Boucias, N.Olmo, M.Oñaderra, and J.G.Gavilanes (2008).
The insecticidal protein hirsutellin A from the mite fungal pathogen Hirsutella thompsonii is a ribotoxin.
  Proteins, 72, 217-228.  
17253975 J.Lacadena, E.Alvarez-García, N.Carreras-Sangrà, E.Herrero-Galán, J.Alegre-Cebollada, L.García-Ortega, M.Oñaderra, J.G.Gavilanes, and A.Martínez del Pozo (2007).
Fungal ribotoxins: molecular dissection of a family of natural killers.
  FEMS Microbiol Rev, 31, 212-237.  
16740124 E.Alvarez-García, L.García-Ortega, Y.Verdún, M.Bruix, A.Martínez del Pozo, and J.G.Gavilanes (2006).
Tyr-48, a conserved residue in ribotoxins, is involved in the RNA-degrading activity of alpha-sarcin.
  Biol Chem, 387, 535-541.  
16791739 N.Powers, and J.H.Jensen (2006).
Chemically accurate protein structures: validation of protein NMR structures by comparison of measured and predicted pKa values.
  J Biomol NMR, 35, 39-51.  
16456030 N.Spacková, and J.Sponer (2006).
Molecular dynamics simulations of sarcin-ricin rRNA motif.
  Nucleic Acids Res, 34, 697-708.  
16231289 H.Li, A.D.Robertson, and J.H.Jensen (2005).
Very fast empirical prediction and rationalization of protein pKa values.
  Proteins, 61, 704-721.  
16110800 K.V.Clemons, and D.A.Stevens (2005).
The contribution of animal models of aspergillosis to understanding pathogenesis, therapy and virulence.
  Med Mycol, 43, S101-S110.  
15885102 L.Garciá-Ortega, J.Lacadena, M.Villalba, R.Rodríguez, J.F.Crespo, J.Rodríguez, C.Pascual, N.Olmo, M.Oñaderra, A.M.del Pozo, and J.G.Gavilanes (2005).
Production and characterization of a noncytotoxic deletion variant of the Aspergillus fumigatus allergen Aspf1 displaying reduced IgE binding.
  FEBS J, 272, 2536-2544.  
15812638 M.F.García-Mayoral, D.Pantoja-Uceda, J.Santoro, A.Martínez del Pozo, J.G.Gavilanes, M.Rico, and M.Bruix (2005).
Refined NMR structure of alpha-sarcin by 15N-1H residual dipolar couplings.
  Eur Biophys J, 34, 1057-1065.  
15653429 A.Siemer, M.Masip, N.Carreras, L.García-Ortega, M.Oñaderra, M.Bruix, A.M.Del Pozo, and J.G.Gavilanes (2004).
Conserved asparagine residue 54 of alpha-sarcin plays a role in protein stability and enzyme activity.
  Biol Chem, 385, 1165-1170.  
15044731 M.F.García-Mayoral, L.García-Ortega, M.P.Lillo, J.Santoro, A.Martínez del Pozo, J.G.Gavilanes, M.Rico, and M.Bruix (2004).
NMR structure of the noncytotoxic alpha-sarcin mutant Delta(7-22): the importance of the native conformation of peripheral loops for activity.
  Protein Sci, 13, 1000-1011.
PDB code: 1r4y
12493839 M.Masip, L.García-Ortega, N.Olmo, M.F.García-Mayoral, J.M.Pérez-Cañadillas, M.Bruix, M.Oñaderra, A.Martínez del Pozo, and J.G.Gavilanes (2003).
Leucine 145 of the ribotoxin alpha-sarcin plays a key role for determining the specificity of the ribosome-inactivating activity of the protein.
  Protein Sci, 12, 161-169.  
12228255 J.Sevcik, L.Urbanikova, P.A.Leland, and R.T.Raines (2002).
X-ray structure of two crystalline forms of a streptomycete ribonuclease with cytotoxic activity.
  J Biol Chem, 277, 47325-47330.
PDB codes: 1mgr 1mgw
11897788 L.Garcia-Ortega, M.Masip, J.M.Mancheño, M.Oñaderra, M.A.Lizarbe, M.F.García-Mayoral, M.Bruix, A.Martínez del Pozo, and J.G.Gavilanes (2002).
Deletion of the NH2-terminal beta-hairpin of the ribotoxin alpha-sarcin produces a nontoxic but active ribonuclease.
  J Biol Chem, 277, 18632-18639.  
11455593 D.Laurents, J.M.Pérez-Cañadillas, J.Santoro, M.Rico, D.Schell, C.N.Pace, and M.Bruix (2001).
Solution structure and dynamics of ribonuclease Sa.
  Proteins, 44, 200-211.
PDB code: 1c54
11468362 L.García-Ortega, J.Lacadena, J.M.Mancheño, M.Oñaderra, R.Kao, J.Davies, N.Olmo, Pozo AM, and J.G.Gavilanes (2001).
Involvement of the amino-terminal beta-hairpin of the Aspergillus ribotoxins on the interaction with membranes and nonspecific ribonuclease activity.
  Protein Sci, 10, 1658-1668.  
11733014 M.Masip, J.Lacadena, J.M.Mancheño, M.Oñaderra, A.Martínez-Ruiz, A.Martínez del Pozo, and J.G.Gavilanes (2001).
Arginine 121 is a crucial residue for the specific cytotoxic activity of the ribotoxin alpha-sarcin.
  Eur J Biochem, 268, 6190-6196.  
11277935 N.Olmo, J.Turnay, G.González de Buitrago, I.López de Silanes, J.G.Gavilanes, and M.A.Lizarbe (2001).
Cytotoxic mechanism of the ribotoxin alpha-sarcin. Induction of cell death via apoptosis.
  Eur J Biochem, 268, 2113-2123.  
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.