<p>Gene fusion products involving protein kinases are known drivers in human cancers and actionable targets for personalized therapy, yet the structural and molecular determinants that control their function are largely unexplored. Here we show that a CCDC6-RET fusion protein, a driver and therapeutic target in lung and thyroid cancers, is a highly active dimeric kinase. Time-resolved mass spectrometry together with a robust biochemical and biophysical characterization reveal that CCDC6-RET functions as a dual ATP- and ADP-dependent kinase able to bind both nucleotides and to use them as phosphoryl donors. We also identify a crosstalk between the C-terminal and the activation segments controlling both the processing and the catalytic activity of the fusion protein. Furthermore, a 3D-structural assembly of a CCDC6-RET homodimer was generated combining single particle electron microscopy, small-angle X-ray scattering and in silico molecular dynamics simulations. Our structural model together with cross-linking mass spectrometry data demonstrated that CCDC6-RET in the inactive state forms a face-to-face dimer characterized by intermolecular-crosslinked activation segments. Upon nucleotide binding the catalytic domains swing apart and fast activation loop phosphorylation could be driven by a mechanism in cis. Our work uncovers the molecular and structural determinants that control the mechanism of CCDC6-RET autoactivation.</p>