Journal:Acta Cryst D:S2059798319002304

The third structural switch in the molecule of archaeal translation initiation factor 2 and its possible role in initiation of GTP hydrolysis and removal of aIF2 from the ribosome

Oleg Nikonov, Olesya Kravchenko, Natalia Nevskaya, Elena Stolboushkina, Maria Garber and Stanislav Nikonov ^[1]

Molecular Tour
Translation initiation factor 2 (e/aIF2) is essential and highly conserved in Eukarya and Archaea. In complex with GTP it is responsible for the positioning of methionylated initiator tRNA (Met-tRNAi) in the initiation complex (IC) of the ribosome. After start codon recognition the factor turns into GDP-bound form, loses affinity for Met-tRNAi and dissociates from IC. Met-tRNAi remains in the P site of the small ribosomal subunit and allows the subsequent steps of initiation process to occur. The factor consists of three subunits: alpha, beta and gamma. The largest gamma subunit (e/aIF2gamma) forms the core of the heterotrimer. It binds the alpha and beta subunits and plays the crucial role in the functioning of the protein. The gamma subunit is a G-protein and consists of three domains. Domain I (G domain) is catalytic and contains a nucleotide binding pocket and two switch regions involved in the GTP hydrolysis and the exchange of GDP to GTP. In this work, the structure of aIF2gamma from Sulfolobus solfataricus obtained in the absence of magnesium ions clarified two important problems of translation initiation: (i) magnesium ion is necessary for the formation of the active GTP-bound form of the gamma subunit. In its absence, switch 1 cannot take the form of an alpha helix and shield the phosphate moiety of GTP from the solvent and (ii) a structural motif capable of accepting two different conformations and containing strongly conserved amino acid residues was found in the domain II of the aIF2gamma and called switch 3. This switch possibly allows the codon-anticodon recognition signal to be transmitted to switch 1, causing the necessary rearrangement of this switch, which leads to the start of GTP hydrolysis and dissociation aIF2 from IC.

Two views of SsoIF2gamma-GDPCP molecules in unit cell of the crystal (6h6k). Molecules are colored: A-cyan, B-magenta, C-green, D-yellow and E-red.

• a) .
• b) .

Closed and open conformations of switch 3 in SsoIF2γ. of the presented structure (6h6k). The γL1 loop of molecule A is shown in cyan and that of molecule E in yellow. The new β-strand 310–312 (shown in green) formed by switch 3 in the closed conformation is antiparallel to strand 258–260 (marked in magenta).

of the molecule E (blue) of the presented structure and the SsoIF2gamma-GDPCP complex obtained in the presence of Mg2+ (PDB code 4rjl, orange). The nucleotide, residues Thr23, Ser35, Thr46 and the hydrogen bonds formed by them are shown only for molecule E. Side chains of Ser35 and Thr46 approach, distorting the portion of switch 1 located between them.

PDB references: The structure of the FKR mutant of the archaeal translation initiation factor 2 gamma subunit in complex with GDPCP, obtained in the absence of magnesium salts in the crystallization solution 6h6k; Gamma subunit of the translation initiation factor 2 from Sulfolobus solfataricus in complex with GDP and formate ion 6i5m.

References

1. ↑ Nikonov O, Kravchenko O, Nevskaya N, Stolboushkina E, Garber M, Nikonov S. The third structural switch in the archaeal translation initiation factor 2 (aIF2) molecule and its possible role in the initiation of GTP hydrolysis and the removal of aIF2 from the ribosome. Acta Crystallogr D Struct Biol. 2019 Apr 1;75(Pt 4):392-399. doi:, 10.1107/S2059798319002304. Epub 2019 Mar 28. PMID:30988256 doi:http://dx.doi.org/10.1107/S2059798319002304