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B12 cofactors directly stabilize an mRNA regulatory switch


Structures of riboswitch receptor domains bound to their effector have shown how messenger RNAs recognize diverse small molecules, but mechanistic details linking the structures to the regulation of gene expression remain elusive1,2. To address this, here we solve crystal structures of two different classes of cobalamin (vitamin B12)-binding riboswitches that include the structural switch of the downstream regulatory domain. These classes share a common cobalamin-binding core, but use distinct peripheral extensions to recognize different B12 derivatives. In each case, recognition is accomplished through shape complementarity between the RNA and cobalamin, with relatively few hydrogen bonding interactions that typically govern RNA–small molecule recognition. We show that a composite cobalamin–RNA scaffold stabilizes an unusual long-range intramolecular kissing-loop interaction that controls mRNA expression. This is the first, to our knowledge, riboswitch crystal structure detailing how the receptor and regulatory domains communicate in a ligand-dependent fashion to regulate mRNA expression.

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Figure 1: Structures of cobalamins and cobalamin riboswitches.
Figure 2: Crystal structures of two distinct cobalamin riboswitches.
Figure 3: Cobalamin recognition by the receptor domain.
Figure 4: Formation of the kissing-loop interaction is the basis of cobalamin-dependent regulatory activity.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factors have been deposited in the Protein Data Bank (PDB) under accession numbers 4FRG (env8AqCbl(ΔJ1/13,P13)), 4FRN (env8AqCbl) and 4GMA (TteAdoCbl).


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This work was supported by grants from the National Institutes of Health (GM073850 and 1S10RR026516) to R.T.B. and by a Colorado Diversity Initiative Fellowship and NIH Ruth L. Kirschstein fellowship (F32GM095121) to J.E.J. The Advanced Light Source is supported by the Director, Office of Science, Office of Basic Energy Sciences, of the US Department of Energy under contract no. DE-AC02-05CH11231.

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Authors and Affiliations



F.E.R. discovered the specificity of the AqCbl class and performed all aspects of the crystallography with assistance from J.T.P.; J.E.J. performed all biochemical experiments and fully characterized the specificities of the cobalamin family; J.T.P. obtained all in vivo data; and all authors contributed to the analysis of the data and the writing of this paper.

Corresponding authors

Correspondence to Francis E. Reyes or Robert T. Batey.

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Competing interests

R.T.B. is a member of the Scientific Advisory Board of BioRelix, a company pursuing the development of antimicrobials that target riboswitches.

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This file contains Supplementary Figures 1-12, Supplementary Tables 1-3 and additional references. (PDF 27942 kb)

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Johnson Jr, J., Reyes, F., Polaski, J. et al. B12 cofactors directly stabilize an mRNA regulatory switch. Nature 492, 133–137 (2012).

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