Crystal structure of RNase Sa3, cytotoxic microbial ribonuclease

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 

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This is version 1.3 of the entry. See complete history


Links X-ray Structure of Two Crystalline Forms of a Streptomycete Ribonuclease with Cytotoxic Activity

Sevcik, J.Urbanikova, L.Leland, P.A.Raines, R.T.

(2002) J Biol Chem 277: 47325-47330

  • DOI: https://doi.org/10.1074/jbc.M208425200
  • Primary Citation of Related Structures:  
    1MGR, 1MGW

  • PubMed Abstract: 

    Ribonuclease (RNase) Sa3 is secreted by the Gram-positive bacterium Streptomyces aureofaciens. The enzyme catalyzes the cleavage of RNA on the 3' side of guanosine residues. Here, x-ray diffraction analysis was used to determine the three-dimensional structure of two distinct crystalline forms of RNase Sa3 to a resolution of 2.0 and 1.7 A. These two structures are similar to each other as well as to that of a homolog, RNase Sa. All of the key active-site residues of RNase Sa (Asn(42), Glu(44), Glu(57), Arg(72), and His(88)) are located in the putative active site of RNase Sa3. Also herein, RNase Sa3 is shown to be toxic to human erythroleukemia cells in culture. Like onconase, which is an amphibian ribonuclease in Phase III clinical trials as a cancer chemotherapeutic, RNase Sa3 is not inhibited by the cytosolic ribonuclease inhibitor protein. Thus, a prokaryotic ribonuclease can be toxic to mammalian cells.

  • Organizational Affiliation

    Institute of Molecular Biology, Slovak Academy of Sciences, Dubravska cesta 21, 84251 Bratislava, Slovak Republic. umbisevc@savba.sk

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Guanyl-specific ribonuclease Sa399Kitasatospora aureofaciensMutation(s): 0 
Gene Names: rnaSA3
EC: (PDB Primary Data), (UniProt)
Find proteins for P30289 (Kitasatospora aureofaciens)
Explore P30289 
Go to UniProtKB:  P30289
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30289
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on LI

Download Ideal Coordinates CCD File 
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.72α = 90
b = 64.72β = 90
c = 69.57γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-04
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model