The yeast Tap42 and mammalian a4 proteins belong to a highly conserved family of regulators of the type 2A phosphatases, which participate in the rapamycin-sensitive signaling pathway, connecting nutrient availability to cell growth. The mechanism of regulation involves binding of Tap42 to Sit4 and PPH21/22 in yeast and binding of a4 to the catalytic subunits of type 2A-related phosphatases PP2A, PP4 and PP6 in mammals. Both recombinant proteins undergo partial proteolysis, generating stable N-terminal fragments. The full-length proteins and a4 C-terminal deletion mutants at amino acids 222 (a4D222), 236 (a4D236) and 254 (a4D254) were expressed in E. coli. a4D254 undergoes proteolysis, producing a fragment similar to the one generated by full-length a4, whereas a4D222 and a4D236 are highly stable proteins. a4 and Tap42 show a-helical circular dichroism spectra, as do their respective N-terminal proteolysis resistant products. The cloned truncated proteins a4D222 and a4D236, however, possess a higher content of a-helix, indicating that the C-terminal region is less structured, which is consistent with its higher sensitivity to proteolysis. In spite of their higher secondary structure content, a4D222 and a4D236 showed thermal unfolding kinetics similar to the full-length a4. Based on small angle X-ray scattering (SAXS), the calculated radius of gyration for a4 and Tap42 were 41.2+/-0.8 A and 42.8+/-0.7 A and their maximum dimension approximately 142 A and approximately 147 A, respectively. The radii of gyration for a4D222 and a4D236 were 21.6+/-0.3 A and 25.7+/-0.2 A, respectively. Kratky plots show that all studied proteins show variable degree of compactness. Calculation of model structures based on SAXS data showed that a4D222 and a4D236 proteins have globular conformation, whereas a4 and Tap42 exhibit elongated shapes.