3F8G

The X-ray structure of a dimeric variant of human pancreatic ribonuclease with high cytotoxic and antitumor activities


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.215 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural features for the mechanism of antitumor action of a dimeric human pancreatic ribonuclease variant.

Merlino, A.Avella, G.Di Gaetano, S.Arciello, A.Piccoli, R.Mazzarella, L.Sica, F.

(2009) Protein Sci 18: 50-57

  • DOI: 10.1002/pro.6
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • A specialized class of RNases shows a high cytotoxicity toward tumor cell lines, which is critically dependent on their ability to reach the cytosol and to evade the action of the ribonuclease inhibitor (RI). The cytotoxicity and antitumor activity o ...

    A specialized class of RNases shows a high cytotoxicity toward tumor cell lines, which is critically dependent on their ability to reach the cytosol and to evade the action of the ribonuclease inhibitor (RI). The cytotoxicity and antitumor activity of bovine seminal ribonuclease (BSRNase), which exists in the native state as an equilibrium mixture of a swapped and an unswapped dimer, are peculiar properties of the swapped form. A dimeric variant (HHP2-RNase) of human pancreatic RNase, in which the enzyme has been engineered to reproduce the sequence of BSRNase helix-II (Gln28-->Leu, Arg31-->Cys, Arg32-->Cys, and Asn34-->Lys) and to eliminate a negative charge on the surface (Glu111-->Gly), is also extremely cytotoxic. Surprisingly, this activity is associated also to the unswapped form of the protein. The crystal structure reveals that on this molecule the hinge regions, which are highly disordered in the unswapped form of BSRNase, adopt a very well-defined conformation in both subunits. The results suggest that the two hinge peptides and the two Leu28 side chains may provide an anchorage to a transient noncovalent dimer, which maintains Cys31 and Cys32 of the two subunits in proximity, thus stabilizing a quaternary structure, similar to that found for the noncovalent swapped dimer of BSRNase, that allows the molecule to escape RI and/or to enhance the formation of the interchain disulfides.


    Related Citations: 
    • Structure and stability of the non-covalent swapped dimer of bovine seminal ribonuclease: an enzyme tailored to evade ribonuclease protein inhibitor.
      Sica, F., Di Fiore, A., Merlino, A., Mazzarella, L.
      (2004) J Biol Chem 279: 36753
    • The buried diversity of bovine seminal ribonuclease: shape and cytotoxicity of the swapped non-covalent form of the enzyme.
      Merlino, A., Ercole, C., Picone, D., Pizzo, E., Mazzarella, L., Sica, F.
      (2008) J Mol Biol 376: 427
    • A dimeric mutant of human pancreatic ribonuclease with selective cytotoxicity toward malignant cells.
      Piccoli, R., Di Gaetano, S., De Lorenzo, C., Grauso, M., Monaco, C., Spalletti-Cernia, D., Laccetti, P., Cinatl, J., Matousek, J., D'Alessio, G.
      (1999) Proc Natl Acad Sci U S A 96: 7768
    • Second generation antitumour human RNase: significance of its structural and functional features for the mechanism of antitumour action.
      Di Gaetano, S., D'alessio, G., Piccoli, R.
      (2001) Biochem J 358: 241

    Organizational Affiliation

    Dipartimento di Chimica, Università degli Studi di Napoli Federico II, Via Cintia, Napoli 80126, Italy.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease pancreatic
A, B
125Homo sapiensMutation(s): 5 
Gene Names: RNASE1RIB1RNS1
EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
Find proteins for P07998 (Homo sapiens)
Go to UniProtKB:  P07998
NIH Common Fund Data Resources
PHAROS  P07998
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.306 
  • R-Value Work: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.855α = 90
b = 78.256β = 90
c = 80.695γ = 90
Software Package:
Software NamePurpose
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-02-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance