6HC5

The structure of the G. violaceus guanidine II riboswitch P2 stem-loop with audouine

Summary for 6HC5

• Entry DOI: 10.2210/pdb6hc5/pdb
• Descriptor: RNA (5'-R(*GP*GP*UP*GP*GP*GP*GP*AP*CP*GP*AP*CP*CP*CP*CP*AP*(CBV)P*C)-3'), SULFATE ION, SODIUM ION, ... (5 entities in total)
• Functional Keywords: guanidine ii riboswitch, stem-loop, tetra loop, dimer, rna
• Biological source: Gloeobacter violaceus
• Total number of polymer chains: 1
• Total formula weight: 6231.73

Authors

Huang, L.,Lilley, D.M.J. (deposition date: 2018-08-14, release date: 2019-02-20, Last modification date: 2024-05-15)

Primary citation

Huang, L.,Wang, J.,Wilson, T.J.,Lilley, D.M.J.
Structure-guided design of a high-affinity ligand for a riboswitch.
Rna, 25:423-430, 2019

PubMed Abstract: We have designed structure-based ligands for the guanidine-II riboswitch that bind with enhanced affinity, exploiting the twin binding sites created by loop-loop interaction. We synthesized diguanidine species, comprising two guanidino groups covalently connected by C linkers where = 4 or 5. Calorimetric and fluorescent analysis shows that these ligands bind with a 10-fold higher affinity to the riboswitch compared to guanidine. We determined X-ray crystal structures of the riboswitch bound to the new ligands, showing that the guanidino groups are bound to both nucleobases and backbone within the binding pockets, analogously to guanidine binding. The connecting chain passes through side openings in the binding pocket and traverses the minor groove of the RNA. The combination of the riboswitch loop-loop interaction and our novel ligands has potential applications in chemical biology.

PubMed: 30609994
DOI: 10.1261/rna.069567.118

Experimental method

X-RAY DIFFRACTION (1.413 Å)