6E1V

Crystal structure of a class I PreQ1 riboswitch complexed with a synthetic compound 3: 2-[(9H-carbazol-3-yl)oxy]-N,N-dimethylethan-1-amine

Summary for 6E1V

• Entry DOI: 10.2210/pdb6e1v/pdb
• Descriptor: RNA (33-MER), 2-[(9H-carbazol-3-yl)oxy]-N,N-dimethylethan-1-amine (3 entities in total)
• Functional Keywords: preq1 riboswitch, synthetic compound, complex, rna
• Biological source: Caldanaerobacter subterraneus subsp. tengcongensis
• Total number of polymer chains: 1
• Total formula weight: 10478.43

Authors

Numata, T.,Connelly, C.M.,Schneekloth, J.S.,Ferre-D'Amare, A.R. (deposition date: 2018-07-10, release date: 2019-04-10, Last modification date: 2023-10-11)

Primary citation

Connelly, C.M.,Numata, T.,Boer, R.E.,Moon, M.H.,Sinniah, R.S.,Barchi, J.J.,Ferre-D'Amare, A.R.,Schneekloth Jr., J.S.
Synthetic ligands for PreQ1riboswitches provide structural and mechanistic insights into targeting RNA tertiary structure.
Nat Commun, 10:1501-1501, 2019

PubMed Abstract: Riboswitches are naturally occurring RNA aptamers that regulate gene expression by binding to specific small molecules. Riboswitches control the expression of essential bacterial genes and are important models for RNA-small molecule recognition. Here, we report the discovery of a class of synthetic small molecules that bind to PreQ riboswitch aptamers. These molecules bind specifically and reversibly to the aptamers with high affinity and induce a conformational change. Furthermore, the ligands modulate riboswitch activity through transcriptional termination despite no obvious chemical similarity to the cognate ligand. X-ray crystallographic studies reveal that the ligands share a binding site with the cognate ligand but make different contacts. Finally, alteration of the chemical structure of the ligand causes changes in the mode of RNA binding and affects regulatory function. Thus, target- and structure-based approaches can be used to identify and understand the mechanism of synthetic ligands that bind to and regulate complex, folded RNAs.

PubMed: 30940810
DOI: 10.1038/s41467-019-09493-3

Experimental method

X-RAY DIFFRACTION (2.56 Å)