Figure 4. Partial structural mimicry of the tRNA-like domain of tmRNA with canonical tRNAs (viewed on preceeding page).

Figure 4

Partial structural mimicry of the tRNA-like domain of tmRNA with canonical tRNAs (viewed on preceeding page). In tmRNA, the structural elements that are colored onto the secondary structure are structurally related with canonical tRNAs. Based on transient electric birefringence studies of an extended version of the tRNA-like domain of E.coli tmRNA, the inter-stem angle between H1-H6 (the acceptor stem) and H5 is a111-137 degrees whereas based on X-ray structures of canonical tRNAs, the angle between the acceptor branch and the anticodon branch is narrower. Representative model of tmRNA tRNA-like structure,26 compared to the X-ray structure of yeast tRNAAsp.58 The acceptor and T stems in both RNAs are in red, T-loops are in green, the tRNA D-loop and the tmRNA D-like loop are both in blue. The secondary structure of the tRNA-like structure of E. coli tmRNA as presented slightly deviates from that proposed in the 3D-model, since a two-base pair stem capping H5 is not supported by the phylogeny. In the 3D-model, connecting nucleotides between the two branches of the L are in yellow and orange, red ribbons follow the ribose-phosphate backbone and the red bars are the base pairs.

From: Protein Tagging and Ribosome Rescue in Bacteria Requires the Recognition of Transfer-Messenger RNA by an Aminoacyl-tRNA Synthetase

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