4FRG: Crystal Structure Of The Cobalamin Riboswitch Aptamer Domain

Citation:
Abstract
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.
PDB ID: 4FRGDownload
MMDB ID: 104080
PDB Deposition Date: 2012/6/26
Updated in MMDB: 2012/12
Experimental Method:
x-ray diffraction
Resolution: 2.95  Å
Source Organism:
Biological Unit for 4FRG: monomeric; determined by author and by software (PISA)
Molecular Components in 4FRG
Label Count Molecule
Nucleotide(1 molecule)
1
Cobalamin Riboswitch Aptamer Domain
Molecule annotation
Chemicals (13 molecules)
1
1
2
5
3
7
* Click molecule labels to explore molecular sequence information.

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