Structure of trigger factor binding domain in biologically homologous complex with eubacterial ribosome reveals its chaperone action

Abstract

Trigger factor (TF), the first chaperone in eubacteria to encounter the emerging nascent chain, binds to the large ribosomal subunit in the vicinity of the protein exit tunnel opening and forms a sheltered folding space. Here, we present the 3.5-A crystal structure of the physiological complex of the large ribosomal subunit from the eubacterium Deinococcus radiodurans with the N-terminal domain of TF (TFa) from the same organism. For anchoring, TFa exploits a small ribosomal surface area in the vicinity of proteins L23 and L29, by using its "signature motif" as well as additional structural elements. The molecular details of TFa interactions reveal that L23 is essential for the association of TF with the ribosome and may serve as a channel of communication with the nascent chain progressing in the tunnel. L29 appears to induce a conformational change in TFa, which results in the exposure of TFa hydrophobic patches to the opening of the ribosomal exit tunnel, thus increasing its affinity for hydrophobic segments of the emerging nascent polypeptide. This observation implies that, in addition to creating a protected folding space for the emerging nascent chain, TF association with the ribosome prevents aggregation by providing a competing hydrophobic environment and may be critical for attaining the functional conformation necessary for chaperone activity.

Fig. 1.

The structure of TFa in complex with D50S. (Left) A side view of the large ribosomal subunit of D. radiodurans (represented by purple-brown RNA backbone and purple-pink ribosomal proteins main chains) with the bound TFa (orange) on a modeled (as in ref. 13) polypeptide chain (green surface). Ribosomal proteins L29 and L23 are highlighted in magenta and blue, respectively. (Right) A view into the ribosomal tunnel. Colors the same as in Left. Note the elongated loop of L23, a unique eubacterial feature, which reaches the interior of the tunnel, to a location allowing its interaction with the emerging nascent chain (in Left).

Fig. 2.

The crystallographic structure of bound TFa. (a) Structure of TFa upon association with the ribosome. (b) An unbiased 2F_o – F_c electron density map around helix A1, contoured at 1.5σ.

Fig. 3.

Conformational rearrangements in TFa upon its association with the ribosome. In all images TFa is represented by its main chain, whereas the ribosomal components are shown as space-filling entities. Bound TFa, orange; unbound TFa, green; L23, blue; L29, magenta; 23S rRNA, light gray. (a) Superposition of the folds of unbound and bound TFa. To obtain this image, loop L1 and helix A1 of the unbound TFa (from PDB ID code 1OMS) were aligned with those of the bound TFa. (b) A view into the ribosomal tunnel highlighting the relative positioning of TFa, L23, and L29. (c) A view from the tunnel into the exposed hydrophobic pocket, created by the bound conformation of TFa. Note the β-sheet region, placed farthest from the actual tunnel opening (see Fig. 1 Left). (d) A hypothetical view of the structure that would been formed by TFa binding at its unbound conformation, indicating that the unbound conformation could not create a folding pocket. Tunnel orientation is as in b.

Fig. 4.

Detailed molecular interactions of TFa (orange) with ribosomal proteins L23 (blue) (a and b) and L29 (magenta) (c).