Cap-free structure of eIF4E suggests a basis for conformational regulation by its ligands

Abstract

The activity of the eukaryotic translation initiation factor eIF4E is modulated through conformational response to its ligands. For example, eIF4G and eIF4E-binding proteins (4E-BPs) modulate cap affinity, and thus physiological activity of eIF4E, by binding a site distal to the 7-methylguanosine cap-binding site. Further, cap binding substantially modulates eIF4E's affinity for eIF4G and the 4E-BPs. To date, only cap-bound eIF4E structures were reported. In the absence of structural information on the apo form, the molecular underpinnings of this conformational response mechanism cannot be established. We report here the first cap-free eIF4E structure. Apo-eIF4E exhibits structural differences in the cap-binding site and dorsal surface relative to cap-eIF4E. Analysis of structure and dynamics of apo-eIF4E, and changes observed upon ligand binding, reveal a molecular basis for eIF4E's conformational response to these ligands. In particular, alterations in the S4-H4 loop, distal to either the cap or eIF4G binding sites, appear key to modulating these effects. Mutation in this loop mimics these effects. Overall, our studies have important implications for the regulation of eIF4E.

Structural characterization of the Z RING-eIF4E complex reveals a distinct mode of control for eIF4E

“…The RING class of eIF4E partners were the first class observed to reduce the affinity of eIF4E for the cap (26). In contrast to Z, eIF4G binding increases the affinity of eIF4E for the cap (27). Binding footprints of Z and the eIF4G peptide (eIF4Gp) from our NMR data indicate that they bind overlapping but distinct surfaces on eIF4E ( Fig.…”

“…Studies of apo eIF4E and the eIF4E-cap complex showed that W102 rotates into the cap-binding site, whereas W56 and its adjacent loop moves as a hinge and together these tryptophans sandwich the m 7 G cap (27). Neither Z nor eIF4Gp perturbed W56 or W102 indole resonances.…”

eIF4E3 acts as a tumor suppressor by utilizing an atypical mode of methyl-7-guanosine cap recognition

“…2C. The rmsd for regions that are not mobile or involved in cap binding is 1.2 Å: thus, similar to eIF4E1 only local changes, not global changes, are induced upon m 7 G-cap binding (8,17). Regions of eIF4E3 important for m 7 G-cap binding (Fig.…”

“…It is likely that this mutant, where alanine cannot act as an Ncap, destabilizes helix formation, which in turn is important for positioning Cys52 and the S1-S2 loop for favorable interactions with m 7 GDP. All cap-bound structures of eIF4E1 show that Trp56 (equivalent to Cys52) forms a small helix, but this helix is not present in the apo structure (8). Preforming of this helix in apo-eIF4E3 likely makes the cap interaction more energetically favorable.…”

“…Specific cap recognition is key for the fate of transcripts and impacts processes such as mRNA processing and bulk mRNA export via the CBC or the nuclear export of specific transcripts as well as bulk translation by eIF4E (5). NMR and crystallographic studies reveal that m 7 G cap is specifically recognized by both the CBC and eIF4E via intercalation of the m 7 G cap moiety with the side chains of two aromatic residues, i.e., an aromatic sandwich (4,(6)(7)(8)(9). This is an electrostatically driven process relying on the partial positive charge of the m 7 G cap and the negative π-electron clouds of the aromatic residues.…”