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. 2007 Nov 20;104(47):18445-50.
doi: 10.1073/pnas.0706784104. Epub 2007 Nov 13.

Structure of an archaeal heterotrimeric initiation factor 2 reveals a nucleotide state between the GTP and the GDP states

Laure Yatime  1 , Yves Mechulam, Sylvain Blanquet, Emmanuelle Schmitt
Affiliations

Structure of an archaeal heterotrimeric initiation factor 2 reveals a nucleotide state between the GTP and the GDP states

Laure Yatime et al. Proc Natl Acad Sci U S A. .

Abstract

Initiation of translation in eukaryotes and in archaea involves eukaryotic/archaeal initiation factor (e/aIF)1 and the heterotrimeric initiation factor e/aIF2. In its GTP-bound form, e/aIF2 provides the initiation complex with Met-tRNA(i)(Met). After recognition of the start codon by initiator tRNA, e/aIF1 leaves the complex. Finally, e/aIF2, now in a GDP-bound form, loses affinity for Met-tRNA(i)(Met) and dissociates from the ribosome. Here, we report a 3D structure of an aIF2 heterotrimer from the archeon Sulfolobus solfataricus obtained in the presence of GDP. Our report highlights how the two-switch regions involved in formation of the tRNA-binding site on subunit gamma exchange conformational information with alpha and beta. The zinc-binding domain of beta lies close to the guanine nucleotide and directly contacts the switch 1 region. As a result, switch 1 adopts a not yet described conformation. Moreover, unexpectedly for a GDP-bound state, switch 2 has the "ON" conformation. The stability of these conformations is accounted for by a ligand, most probably a phosphate ion, bound near the nucleotide binding site. The structure suggests that this GDP-inorganic phosphate (Pi) bound state of aIF2 may be proficient for tRNA binding. Recently, it has been proposed that dissociation of eIF2 from the initiation complex is closely coupled to that of Pi from eIF2gamma upon start codon recognition. The nucleotide state of aIF2 shown here is indicative of a similar mechanism in archaea. Finally, we consider the possibility that release of Pi takes place after e/aIF2gamma has been informed of e/aIF1 dissociation by e/aIF2beta.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
S. solfataricus aIF2αβγ. (A) Overall structure of aIF2α3βγ bound to GDP. aIF2γ is yellow, switch 1 is red (g-31 to g-49), and switch 2 is orange (g-93 to g-113). The aIF2α3 domain (a-174 to a-266) is cyan. The aIF2β-helix 1 (b-3 to b-17) is green. Residues b-23 to b-27 are not visible. The aIF2β central domain (b-28 to b-103) is dark green, and the aIF2β ZBD (b-104 to b-139) is light green. The same color coding is used in all four structures. (B) Putative structure of the full aIF2αβγ heterotrimer, as deduced from the available data. This structure results from superimposition of aIF2γ, as in the present aIF2α3βγ structure, to aIF2γ, as in the aIF2αγ:GDPNP-Mg2+ structure (20). The three domains of aIF2α are colored as follows: the N-terminal domain is dark blue (a-1 to a-84), the central domain is marine (a-85 to a-173), and the C-terminal domain is cyan (a-174 to a-266). (C) View of aIF2αγ:GDPNP-Mg2+ as obtained in ref. . Residues g-36 to g-43 in switch 1 are not visible. Switch 1 is ON, and the conserved g-T46 contacts the magnesium ion. Switch 2 is ON, and the NH group of g-G96 contacts the γ-phosphate. (D) Overall structure of Ss-aIF2α3β1γ bound to GDP–Mg2+. Residues g-35 to g-48 in switch 1 are not visible. Figs. 1–3 and SI Figs. 7–9 were drawn with PyMol (DeLano Scientific LLC).
Fig. 2.
Fig. 2.
Structure of aIF2β within the Ss-aIF2α3βγ heterotrimer. (A) Overall structure of aIF2β. The color coding is the same as in Fig. 1A. The side chains of residues conserved in e/aIF2β sequences are drawn. C106, C109, C127, C130, V104, N46, and R56 are strictly conserved in all e/aIF2β (30 aIF2β and 43 eIF2β sequences) and eIF5 (60 sequences). Y7 is strictly conserved in all e/aIF2β sequences. L11 is strictly conserved in all aIF2β sequences and can be replaced by V (3 eIF2 sequences) or T (1 eIF2 sequence) in eIF2β. T114 is strictly conserved in the e/aIF2β sequences, but three exceptions exist in eIF5. Either F or Y are systematically found at positions 99 and 103 in e/aIF2β and eIF5. (B) Comparison of Ss-aIF2α3βγ and Pf-aIF2βγ (27) after superimposition of the two aIF2γ-subunits. Ss-aIF2β is green, Ss-aIF2γ is yellow, Ss-aIF2α3 is cyan, Pf-aIF2β is red, and Pf-aIF2γ is gray. This view shows the opposite orientations of the two aIF2β-subunits with respect to aIF2γ.
Fig. 3.
Fig. 3.
Communication between subunits. (A) Interaction of the b-α1-helix of Ss-aIF2β (green) with the G domain of Ss-aIF2γ (yellow). Relevant side chains are drawn. (B) Close-up view of the Ss-aIF2α3βγ heterotrimer highlighting the switch 1-mediated communication between the three subunits. The color coding is the same as that used in Fig. 1. Relevant side chains are drawn. Note the orientations of b-K117, b-E119, and b-Q133 toward the ribose hydroxyls of GDP and the stacking of b-E119 on g-W33.
Fig. 4.
Fig. 4.
Nucleotide binding site. (A) View of the Ss-aIF2α3βγ nucleotide-binding pocket showing the positions of relevant aIF2β and aIF2γ residues, as discussed in the text. The composite annealed 2Fo − Fc omit map was contoured at 1 σ. (B) View of the Ss-aIF2α3β1γ nucleotide-binding pocket, drawn in approximately the same orientation as in A. The composite annealed 2Fo − Fc omit map was contoured at 1 σ. Comparison of A and B shows the differences between the GDP–Pi and the GDP–Mg2+ states. (C) Close-up stereoview of the putative phosphate-binding pocket. The side chains of relevant residues are drawn. The water molecule linking the phosphate group to the NH of g-G96 is drawn as a red sphere. Hydrogen bonds surrounding the Pi group are shown. The 2Fo − Fc map contoured at 1 σ (firebrick) and the Fo − Fc map contoured at 4 σ (blue) were calculated before the addition of the Pi and water molecules in the model. B factors (in Å2) of the atoms coordinating the phosphate (72 Å2) and the water (29 Å2) are as follows: 34 (NH g-G96), 52 (Nδ g-H97), 55 (Nε g-K48), and 63 (Nδ g-H37).
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References

    1. Huang HK, Yoon H, Hannig EM, Donahue TF. Genes Dev. 1997;11:2396–2413. - PMC - PubMed
    1. Phan L, Schoenfeld LW, Valasek L, Nielsen KH, Hinnebusch AG. EMBO J. 2001;20:2954–2965. - PMC - PubMed
    1. Fekete CA, Applefield DJ, Blakely SA, Shirokikh N, Pestova T, Lorsch JR, Hinnebusch AG. EMBO J. 2005;24:3588–3601. - PMC - PubMed
    1. Olsen DS, Savner EM, Mathew A, Zhang F, Krishnamoorthy T, Phan L, Hinnebusch AG. EMBO J. 2003;22:193–204. - PMC - PubMed
    1. Maag D, Fekete CA, Gryczynski Z, Lorsch JR. Mol Cell. 2005;17:265–275. - PubMed

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