Abstract
The k-junction is a structural motif in RNA comprising a three-way helical junction based upon kink turn (k-turn) architecture. A computer program written to examine relative helical orientation identified the three-way junction of the Arabidopsis TPP riboswitch as an elaborated k-turn. The Escherichia coli TPP riboswitch contains a related k-junction, and analysis of >11 000 sequences shows that the structure is common to these riboswitches. The k-junction exhibits all the key features of an N1-class k-turn, including the standard cross-strand hydrogen bonds. The third helix of the junction is coaxially aligned with the C (canonical) helix, while the k-turn loop forms the turn into the NC (non-canonical) helix. Analysis of ligand binding by ITC and global folding by gel electrophoresis demonstrates the importance of the k-turn nucleotides. Clearly the basic elements of k-turn structure are structurally well suited to generate a three-way helical junction, retaining all the key features and interactions of the k-turn.
Highlights
The kink turn (k-turn) is an extremely widespread structural motif that generates a tight kink in duplex RNA [1,2], thereby frequently mediating tertiary interactions
For all helix segments we searched for nearby candidate helical segments that matched the search pattern. Using this approach we observed that the A. thaliana thiamine pyrophosphate (TPP) riboswitch (PDB code 3D2G) contained two helices with a strong structural similarity to the k-turn geometry
The identification of the k-junction in the TPP riboswitches shows that the k-turn is an adaptable motif that can be accommodated within the framework of more complex structural entities
Summary
The kink turn (k-turn) is an extremely widespread structural motif that generates a tight kink in duplex RNA [1,2], thereby frequently mediating tertiary interactions. This is exploited by at least six riboswitch structures to create ligand binding pockets, and there are numerous k-turn structures found in ribosomal RNA species contributing to the architecture of the ribosome [1]. Many k-turns are targets for the binding of specific proteins, including the L7Ae family [3]. The kinked structure of the k-turn requires stabilization, in the absence of which the RNA is relatively extended and probably flexible. K-turn stabilization can occur due to the presence of metal ions for some (but not all) sequences [7], as a result of tertiary interactions [8] or due to the binding of proteins [9,10,11,12]
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