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PDBsum entry 2sar
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protein ligands Protein-protein interface(s) links
Hydrolase (endoribonuclease) PDB id
2sar

 

 

 

 

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Contents
Protein chains
96 a.a. *
Ligands
SO4 ×2
3GP
Waters ×222
* Residue conservation analysis
PDB id:
2sar
Name: Hydrolase (endoribonuclease)
Title: Determination and restrained least-squares refinement of the crystal structures of ribonuclease sa and its complex with 3'-guanylic acid at 1.8 angstroms resolution
Structure: Ribonuclease sa. Chain: a, b. Engineered: yes
Source: Streptomyces aureofaciens. Organism_taxid: 1894
Resolution:
1.80Å     R-factor:   0.175    
Authors: J.Sevcik,E.J.Dodson,G.G.Dodson
Key ref: J.Sevcik et al. (1991). Determination and restrained least-squares refinement of the structures of ribonuclease Sa and its complex with 3'-guanylic acid at 1.8 A resolution. Acta Crystallogr B, 47, 240-253. PubMed id: 1654932
Date:
13-Dec-90     Release date:   15-Apr-92    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P05798  (RNSA_KITAU) -  Guanyl-specific ribonuclease Sa from Kitasatospora aureofaciens
Seq:
Struc: 		96 a.a.
96 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.4.6.1.24  - ribonuclease T1.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: [RNA] containing guanosine + H2O = an [RNA fragment]-3'-guanosine- 3'-phosphate + a 5'-hydroxy-ribonucleotide-3'-[RNA fragment]

 

 
Acta Crystallogr B 47:240-253 (1991)
PubMed id: 1654932  
 
 
Determination and restrained least-squares refinement of the structures of ribonuclease Sa and its complex with 3'-guanylic acid at 1.8 A resolution.
J.Sevcik, E.J.Dodson, G.G.Dodson.
 
  ABSTRACT  
 
The crystal structures of ribonuclease from Streptomyces aureofaciens (RNase Sa) and its complex with 3'-guanylic acid (guanosine 3'-monophosphate, 3'-GMP) have been determined by the method of isomorphous replacement. The atomic parameters have been refined by restrained least-squares minimization using data in the resolution range 10.0-1.8 A. All protein atoms and more than 230 water atoms in the two crystal structures have been refined to crystallographic R factors of 0.172 and 0.175 respectively. The estimated r.m.s. error in the atomic positions ranges from 0.2 A for well-defined atoms to about 0.5 A for more poorly defined atoms. There are two enzyme molecules in the asymmetric unit, built independently, and referred to as molecules A and B. The value of the average B factor for protein atoms in both structures is about 19 A2 and for water molecules about 35 A2. Electron density for the substrate analogue 3'-GMP was found only at the active site of molecule A. The density was very clear and the positions of all 3'-GMP atoms were refined with precision comparable to that of the protein.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20823552 F.Pavelcík, and J.Václavík (2010).
Performance of phased rotation, conformation and translation function: accurate protein model building with tripeptidic and tetrapeptidic fragments.
  Acta Crystallogr D Biol Crystallogr, 66, 1012-1023.  
19558492 V.Bauerová-Hlinková, R.Dvorský, D.Perecko, F.Povazanec, and J.Sevcík (2009).
Structure of RNase Sa2 complexes with mononucleotides--new aspects of catalytic reaction and substrate recognition.
  FEBS J, 276, 4156-4168.
PDB codes: 3d4a 3d5g 3d5i 3dgy 3dh2
19825371 W.Ardelt, B.Ardelt, and Z.Darzynkiewicz (2009).
Ribonucleases as potential modalities in anticancer therapy.
  Eur J Pharmacol, 625, 181-189.  
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.  
16109374 K.Kamada, and F.Hanaoka (2005).
Conformational change in the catalytic site of the ribonuclease YoeB toxin by YefM antitoxin.
  Mol Cell, 19, 497-509.
PDB codes: 2a6q 2a6r 2a6s
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.  
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
10373011 R.Loris, U.Langhorst, S.De Vos, K.Decanniere, J.Bouckaert, D.Maes, T.R.Transue, and J.Steyaert (1999).
Conserved water molecules in a large family of microbial ribonucleases.
  Proteins, 36, 117-134.
PDB codes: 1bu4 2bu4 3bu4 4bu4 5bu4
8069624 C.A.Orengo, and J.M.Thornton (1993).
Alpha plus beta folds revisited: some favoured motifs.
  Structure, 1, 105-120.  
8396032 J.Sevcik, I.Zegers, L.Wyns, Z.Dauter, and K.S.Wilson (1993).
Complex of ribonuclease Sa with a cyclic nucleotide and a proposed model for the reaction intermediate.
  Eur J Biochem, 216, 301-305.
PDB code: 1rsn
8464727 S.L.Moodie, and J.M.Thornton (1993).
A study into the effects of protein binding on nucleotide conformation.
  Nucleic Acids Res, 21, 1369-1380.  
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.

 

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