2PMD

The structures of aIF2gamma subunit from the archaeon Sulfolobus solfataricus in the GDP-bound form.

Summary for 2PMD

• Entry DOI: 10.2210/pdb2pmd/pdb
• Related: 2AHO
• Descriptor: Translation initiation factor 2 gamma subunit, GUANOSINE-5'-DIPHOSPHATE, PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER, ... (5 entities in total)
• Functional Keywords: aif2, initiation factor 2 gamma subunit, initiation of the translation, nucleotide binding, gdpnp, gdp, pyrophosphate, translation
• Biological source: Sulfolobus solfataricus
• Total number of polymer chains: 2
• Total formula weight: 94174.91

Authors

Nikonov, O.S.,Stolboushkina, E.A.,Nikulin, A.D.,Hasenohrl, D.,Blaesi, U.,Manstein, D.J.,Fedorov, R.V.,Garber, M.B.,Nikonov, S.V. (deposition date: 2007-04-21, release date: 2007-11-06, Last modification date: 2024-11-20)

Primary citation

Nikonov, O.,Stolboushkina, E.,Nikulin, A.,Hasenohrl, D.,Blasi, U.,Manstein, D.J.,Fedorov, R.,Garber, M.,Nikonov, S.
New Insights into the Interactions of the Translation Initiation Factor 2 from Archaea with Guanine Nucleotides and Initiator tRNA.
J.Mol.Biol., 373:328-336, 2007

PubMed Abstract: Heterotrimeric a/eIF2alphabetagamma (archaeal homologue of the eukaryotic translation initiation factor 2 with alpha, beta and gamma subunits) delivers charged initiator tRNA (tRNAi) to the small ribosomal subunit. In this work, we determined the structures of aIF2gamma from the archaeon Sulfolobus solfataricus in the nucleotide-free and GDP-bound forms. Comparison of the free, GDP and Gpp(NH)p-Mg2+ forms of aIF2gamma revealed a sequence of conformational changes upon GDP and GTP binding. Our results show that the affinity of GDP to the G domain of the gamma subunit is higher than that of Gpp(NH)p. In analyzing a pyrophosphate molecule binding to domain II of the gamma subunit, we found a cleft that is very suitable for the acceptor stem of tRNA accommodation. It allows the suggestion of an alternative position for Met-tRNA i Met on the alphagamma intersubunit dimer, at variance with a recently published one. In the model reported here, the acceptor stem of the tRNAi is approximately perpendicular to that of tRNA in the ternary complex elongation factor Tu-Gpp(NH)p-tRNA. According to our analysis, the elbow and T stem of Met-tRNA i Met in this position should make extensive contact with the alpha subunit of aIF2. Thus, this model is in good agreement with experimental data showing that the alpha subunit of aIF2 is necessary for the stable interaction of aIF2gamma with Met-tRNA i Met.

PubMed: 17825838
DOI: 10.1016/j.jmb.2007.07.048

Experimental method

X-RAY DIFFRACTION (2.65 Å)