The crystal structure of the domain-swapped dimer of onconase highlights some catalytic and antitumor activity features of the enzyme

Int J Biol Macromol. 2021 Nov 30:191:560-571. doi: 10.1016/j.ijbiomac.2021.09.095. Epub 2021 Sep 24.


Onconase (ONC) is a monomeric amphibian "pancreatic-type" RNase endowed with remarkable anticancer activity. ONC spontaneously forms traces of a dimer (ONC-D) in solution, while larger amounts can be formed when ONC is lyophilized from mildly acidic solutions. Here, we report the crystal structure of ONC-D and analyze its catalytic and antitumor activities in comparison to ONC. ONC-D forms via the three-dimensional swapping of the N-terminal α-helix between two monomers, but it displays a significantly different quaternary structure from that previously modeled [Fagagnini A et al., 2017, Biochem J 474, 3767-81], and based on the crystal structure of the RNase A N-terminal swapped dimer. ONC-D presents a variable quaternary assembly deriving from a variable open interface, while it retains a catalytic activity that is similar to that of ONC. Notably, ONC-D displays antitumor activity against two human melanoma cell lines, although it exerts a slightly lower cytostatic effect than the monomer. The inhibition of melanoma cell proliferation by ONC or ONC-D is associated with the reduction of the expression of the anti-apoptotic B cell lymphoma 2 (Bcl2), as well as of the total expression and phosphorylation of the Signal Transducer and Activator of Transcription (STAT)-3. Phosphorylation is inhibited in both STAT3 Tyr705 and Ser727 key-residues, as well as in its upstream tyrosine-kinase Src. Consequently, both ONC species should exert their anti-cancer action by inhibiting the pro-tumor pleiotropic STAT3 effects deriving either by its phospho-tyrosine activation or by its non-canonical signaling pathways. Both ONC species, indeed, increase the portion of A375 cells undergoing apoptotic cell death. This study expands the variety of RNase domain-swapped dimeric structures, underlining the unpredictability of the open interface arrangement upon domain swapping. Structural data also offer valuable insights to analyze the differences in the measured ONC or ONC-D biological activities.

Keywords: 3D domain swapping; Antitumor activity; Bcl2; Human melanoma; Onconase; Onconase dimer; Ribonuclease; STAT-3; Src kinase.

MeSH terms

  • Antineoplastic Agents / chemistry*
  • Antineoplastic Agents / pharmacology
  • Apoptosis
  • Catalytic Domain*
  • Cell Line, Tumor
  • Cell Proliferation / drug effects
  • Humans
  • Melanoma / metabolism*
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / metabolism
  • Ribonucleases / chemistry*
  • Ribonucleases / metabolism
  • STAT3 Transcription Factor / genetics
  • STAT3 Transcription Factor / metabolism


  • Antineoplastic Agents
  • Recombinant Proteins
  • STAT3 Transcription Factor
  • Ribonucleases
  • ranpirnase