3VRS

Crystal structure of fluoride riboswitch, soaked in Mn2+

Summary for 3VRS

• Entry DOI: 10.2210/pdb3vrs/pdb
• Related: 4EN5 4ENA 4ENB 4ENC
• Descriptor: Fluoride riboswitch, MANGANESE (II) ION, POTASSIUM ION, ... (5 entities in total)
• Functional Keywords: pseudoknot, rna
• Biological source: Thermotoga petrophila
• Total number of polymer chains: 1
• Total formula weight: 17329.58

Authors

Ren, A.M.,Rajashankar, K.R.,Patel, D.J. (deposition date: 2012-04-13, release date: 2012-05-09, Last modification date: 2023-09-13)

Primary citation

Ren, A.,Rajashankar, K.R.,Patel, D.J.
Fluoride ion encapsulation by Mg2+ ions and phosphates in a fluoride riboswitch.
Nature, 486:85-89, 2012

PubMed Abstract: Significant advances in our understanding of RNA architecture, folding and recognition have emerged from structure-function studies on riboswitches, non-coding RNAs whose sensing domains bind small ligands and whose adjacent expression platforms contain RNA elements involved in the control of gene regulation. We now report on the ligand-bound structure of the Thermotoga petrophila fluoride riboswitch, which adopts a higher-order RNA architecture stabilized by pseudoknot and long-range reversed Watson-Crick and Hoogsteen A•U pair formation. The bound fluoride ion is encapsulated within the junctional architecture, anchored in place through direct coordination to three Mg(2+) ions, which in turn are octahedrally coordinated to water molecules and five inwardly pointing backbone phosphates. Our structure of the fluoride riboswitch in the bound state shows how RNA can form a binding pocket selective for fluoride, while discriminating against larger halide ions. The T. petrophila fluoride riboswitch probably functions in gene regulation through a transcription termination mechanism.

PubMed: 22678284
DOI: 10.1038/nature11152

Experimental method

X-RAY DIFFRACTION (2.603 Å)