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 elusive. To address this, here we solve crystal structures of two different classes of cobalamin (vitamin B(12))-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 B(12) 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.
Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado 80309-0596, USA.
James E
JE
Johnson
Francis E
FE
Reyes
Jacob T
JT
Polaski
Robert T
RT
Batey
D001483:Base Sequence; D002151:Calorimetry; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000235:genetics; D005786:Gene Expression Regulation / Q000187:drug effects; D006860:Hydrogen Bonding / Q000187:drug effects; D008024:Ligands; D008958:Models, Molecular; D009690:Nucleic Acid Conformation / Q000187:drug effects*; D012329:RNA, Bacterial / Q000235:genetics; D012333:RNA, Messenger / Q000737:chemistry* / Q000187:drug effects / Q000235:genetics / Q000378:metabolism; D058928:Riboswitch / Q000187:drug effects* / Q000235:genetics; D013816:Thermodynamics; D014805:Vitamin B 12 / Q000737:chemistry* / Q000378:metabolism / Q000494:pharmacology*
D008024:Ligands; D012329:RNA, Bacterial; D012333:RNA, Messenger; D058928:Riboswitch; D014805:Vitamin B 12