1RSN

RIBONUCLEASE (RNASE SA) (E.C.3.1.4.8) COMPLEXED WITH EXO-2',3'-CYCLOPHOSPHOROTHIOATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.119 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Complex of ribonuclease Sa with a cyclic nucleotide and a proposed model for the reaction intermediate.

Sevcik, J.Zegers, I.Wyns, L.Dauter, Z.Wilson, K.S.

(1993) Eur J Biochem 216: 301-305

  • DOI: 10.1111/j.1432-1033.1993.tb18145.x
  • Primary Citation of Related Structures:  
    1RSN

  • PubMed Abstract: 
  • The structure of the complex of ribonuclease from Streptomyces aureofaciens (RNase Sa) with exo guanosine 2',3'-cyclophosphorothioate has been refined against 0.2-nm resolution synchrotron data using, as a starting model, coordinates from the RNase Sa: 2'-GMP complex ...

    The structure of the complex of ribonuclease from Streptomyces aureofaciens (RNase Sa) with exo guanosine 2',3'-cyclophosphorothioate has been refined against 0.2-nm resolution synchrotron data using, as a starting model, coordinates from the RNase Sa: 2'-GMP complex. The refinement was based on all data over 1.0-0.2 nm and converged to a crystallographic R factor of 11.9%. This is the first structure of a microbial ribonuclease complexed with a 2',3'-cyclophosphorothioate, which is a thio analogue of the intermediate of the two-step reaction. However, exo guanosine 2',3'-cyclophosphorothioate is bound in a non-functional mode and is not hydrolysed. This structure therefore does not provide direct evidence on the identity of the amino acid residues responsible for catalytic cleavage of the substrate. However, based on present and previous results, a plausible model is proposed for the complex of the cyclic intermediate which acts as substrate for the second step of the catalysis.


    Related Citations: 
    • Complex of Ribonuclease from Streptomyces Aureofaciens with 2'-Gmp at 1.7 Angstroms Resolution
      Sevcik, J., Hill, C.P., Dauter, Z., Wilson, K.S.
      (1993) Acta Crystallogr D Biol Crystallogr 49: 257
    • Determination and Restrained Least-Squares Refinement of the Structure of Ribonuclease And its Complex with 3'-Guanylic Acid at 1.8 Angstroms Resolution
      Sevcik, J., Dodson, E.J., Dodson, G.G.
      (1991) Acta Crystallogr B 47: 240
    • Comparison of Active Sites of Some Microbial Ribonucleases: Structural Basis for Guanylic Specificity
      Sevcik, J., Sanishvili, R.G., Pavlovsky, A.G., Polyakov, K.M.
      (1990) Trends Biochem Sci 5: 158
    • Amino Acid Sequence Determination of Guanyl-Specific Ribonuclease Sa from Streptomyces Aureofaciens
      Shlyapnikov, S.U., Both, V., Kulikov, V.A., Dementiev, A.A., Sevcik, J., Zelinka, J.
      (1986) FEBS Lett 209: 335
    • Exocellular Ribonuclease from Streptomyces Aureofaciens. I. Isolation and Purification
      Bacova, M., Zelinkova, E., Zelinka, J.
      (1971) Biochim Biophys Acta 235: 335
    • Exocellular Ribonuclease from Streptomyces Aureofaciens. II. Properties and Specificity
      Bacova, M., Zelinkova, E., Zelinka, J.
      (1971) Biochim Biophys Acta 235: 343

    Organizational Affiliation

    Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RIBONUCLEASE SAA, B96Kitasatospora aureofaciensMutation(s): 0 
Gene Names: rnaSA
EC: 3.1.27.3 (PDB Primary Data), 4.6.1.24 (UniProt)
UniProt
Find proteins for P05798 (Kitasatospora aureofaciens)
Explore P05798 
Go to UniProtKB:  P05798
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SGP (Subject of Investigation/LOI)
Query on SGP

Download Ideal Coordinates CCD File 
D [auth A], E [auth B]GUANOSINE-2',3'-CYCLOPHOSPHOROTHIOATE
C10 H12 N5 O6 P S
QZEROIIFJLCOOE-FHIGPPGSSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Observed: 0.119 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.7α = 90
b = 78.8β = 90
c = 39.1γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PROLSQrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-12-07
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance