The three-dimensional chalice-like crystal structure of initiation factor 2 IF2/eIF5B from Methanobacterium thermoautotrophicum represents a novel fold and domain architecture in which the N-terminal G domain and the C-terminal C domain are separated by an ∼40 Å α-helix. Homologous Thermus thermophilus initiation factor 2 (IF2wt), G (IF2G), and C (IF2C) domains were successfully overexpressed and purified which enabled us to perform a thermodynamic analysis and to asses the role of the domain architecture in this atypical fold. Circular dichroism in the far-UV region demonstrated that the proteins are well-folded and that the secondary structure content resembles that of IF2 from M. thermoautotrophicum. IF2wt and IF2G are monomelic proteins, while IF2C has a tendency to form dimeric species as shown by sedimentation velocity studies on analytical ultracentrifugation and differential scanning calorimetry scan analysis. Thermal denaturation studies of multidomain IF2wt reveals an exceptionally high reversibility (>90%) of the transition with a melting temperature of 94.5°C. Melting temperature of IF2wt may be further increased in the presence of its physiological ligand GDP and the GTP analogue, GppNHp. The high reversibility of denaturation is achieved by the modular structure of the protein and by the high reversibility of the thermal denaturation of IF2G. On the other hand, hydrophobic IF2C aggregates during the thermal transition, and the aggregation is suppressed by guanidine hydrochloride. Isothermal denaturation demonstrates that both IF2G and IF2C have comparable stabilities of 46 and 33 kJ/mol, respectively. The apparent cooperative unfolding of the full-length protein has an unusually small denaturant m value. This together with the phase diagram method of analysis indicates the presence of intermediate(s) due to the independent unfolding of IF2G and IF2C. Despite an absence of apparent interactions between the domains in vitro, IF2G plays a role in IF2C reversibility in thermal denaturation. In conclusion, interactions between the domains of folded IF2wt in vivo are likely mediated by their α-helix connection and/or by a conformational change on the ribosome.
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