The adenosylcobalamin riboswitches are both the largest and most broadly distributed of the riboswitches. To understand the function of this RNA, we solved structures of two distinct members of the cobalamin clan. The three-dimensional structure of the Thermoanaerobacter tencongnesisadenosylcobalamin riboswitch with both aptamer domain (blue/cyan/magenta) and the regulatory kissing loop interaction (green).
Hydroxocoblamin riboswitches (class-II): PDB ID 4FRN,4FRG
The minor class of cobalamin riboswitches is much smaller in size and, in the case of this representative, is highly selective for hydroxocoblamin over adenosylcobalamin. However, the core of the aptamer domain (blue) and the regulatory kissing loop interaction (green) are highly similar to that of the first class.
The cobalamin sits in a pocket formed by a four-way junction motif (blue) and the kissing loop interaction (green) between the aptamer domain and expression platform. The variable beta-axial moiety of the cobalamin projects directly towards the four-way junction and this region is central for selectivity for adenosylcobalamin versus hydroxocobalamin.
Most importantly, the hydroxocobalamin riboswitch is the only riboswitch structure that contains all of the sequence elements known to be both necessary and sufficient for regulatory activity. Insertion of this element into the 5' leader of an mRNA reporter expressing GFP demonstrates that the riboswitch strongly represses GFP in the presence of coblamin in the growth media (red line). Elimination of the regulatory kissing loop interaction results in a loss of activity (black).