2YDH

Crystal structure of the SAM-I riboswitch A94G U34 G18U G19U variant in complex with SAM

Summary for 2YDH

• Entry DOI: 10.2210/pdb2ydh/pdb
• Related: 2YGH
• Descriptor: SAM-I RIBOSWITCH, BARIUM ION, S-ADENOSYLMETHIONINE, ... (4 entities in total)
• Functional Keywords: rna, k-turn
• Biological source: THERMOANAEROBACTER TENGCONGENSIS
• Total number of polymer chains: 1
• Total formula weight: 31575.33

Authors

Schroeder, K.T.,Daldrop, P.,Lilley, D.M.J. (deposition date: 2011-03-21, release date: 2011-09-07, Last modification date: 2023-12-20)

Primary citation

Schroeder, K.T.,Daldrop, P.,Lilley, D.M.J.
RNA Tertiary Interactions in a Riboswitch Stabilize the Structure of a Kink Turn.
Structure, 19:1233-, 2011

PubMed Abstract: The kink turn is a widespread RNA motif that introduces an acute kink into the axis of duplex RNA, typically comprising a bulge followed by a G⋅A and A⋅G pairs. The kinked conformation is stabilized by metal ions, or the binding of proteins including L7Ae. We now demonstrate a third mechanism for the stabilization of k-turn structure, involving tertiary interactions within a larger RNA structure. The SAM-I riboswitch contains an essential standard k-turn sequence that kinks a helix so that its terminal loop can make a long-range interaction. We find that some sequence variations in the k-turn within the riboswitch do not prevent SAM binding, despite preventing the folding of the k-turn in isolation. Furthermore, two crystal structures show that the sequence-variant k-turns are conventionally folded within the riboswitch. This study shows that the folded structure of the k-turn can be stabilized by tertiary interactions within a larger RNA structure.

PubMed: 21893284
DOI: 10.1016/J.STR.2011.07.003

Experimental method

X-RAY DIFFRACTION (2.9 Å)