8KEB

Crystal structure of 2'-dG-III riboswitch with 2'-dG

Summary for 8KEB

• Entry DOI: 10.2210/pdb8keb/pdb
• Descriptor: RNA (72-MER), GUANOSINE-5'-TRIPHOSPHATE, 2'-DEOXY-GUANOSINE, ... (6 entities in total)
• Functional Keywords: riboswitch, 2'-deoxyguanosine, 2'-dg, aptamer, rna
• Biological source: Bacillus sp.
• Total number of polymer chains: 1
• Total formula weight: 23886.63

Authors

Liao, W.,Huang, L. (deposition date: 2023-08-11, release date: 2025-02-19, Last modification date: 2025-09-10)

Primary citation

Chen, K.,Liao, W.,Wang, J.,Ren, Y.,Lu, Z.,Peng, X.,Wang, J.,Huang, L.
Crystal structures reveal the distinct features of the 2'-dG-III riboswitch in the purine riboswitch family.
Nucleic Acids Res., 53:-, 2025

PubMed Abstract: Purine riboswitches, located in the 5'-untranslated regions of bacterial messenger RNA, regulate gene expression by sensing purines and their derivatives. A class of the guanine-I riboswitch variants was recently reported to be the third class of 2'-deoxyguanosine (2'-dG) riboswitch termed 2'-dG-III riboswitch. Here we present the crystal structures of the 2'-dG-III riboswitch bound with 2'-dG, guanosine, or guanine. Despite similarities in secondary and overall structures to other purine riboswitches, the 2'-dG-III riboswitch exhibits unique features in its loop-loop interaction, three-way junction, and ligand binding. The 2'-dG-III riboswitch exhibits a tuning fork-like structure with a unique six-tiered interaction within the three-way junction. The second, third, and fourth tiers form the ligand-binding pocket, with a consistent binding mode for the guanine moiety of all three ligands. Structural and biochemical analyses reveal detailed interactions between the 2'-dG-III riboswitch and different ligands, providing insights into its regulatory mechanisms in purine metabolism.

PubMed: 40694847
DOI: 10.1093/nar/gkaf702

Experimental method

X-RAY DIFFRACTION (2.2 Å)