8XZM

Crystal structure of folE riboswitch with DHN

Summary for 8XZM

• Entry DOI: 10.2210/pdb8xzm/pdb
• Descriptor: RNA (53-MER), MAGNESIUM ION, 2-AMINO-7,8-DIHYDRO-6-(1,2,3-TRIHYDROXYPROPYL)-4(1H)-PTERIDINONE, ... (5 entities in total)
• Functional Keywords: riboswitch, dhn, rna
• Biological source: unidentified eubacterium clone A70
• Total number of polymer chains: 1
• Total formula weight: 17753.14

Authors

Li, C.Y.,Ren, A.M. (deposition date: 2024-01-21, release date: 2024-07-24, Last modification date: 2024-08-21)

Primary citation

Li, C.,Xu, X.,Geng, Z.,Zheng, L.,Song, Q.,Shen, X.,Wu, J.,Zhao, J.,Li, H.,He, M.,Tai, X.,Zhang, L.,Ma, J.,Dong, Y.,Ren, A.
Structure-based characterization and compound identification of the wild-type THF class-II riboswitch.
Nucleic Acids Res., 52:8454-8465, 2024

PubMed Abstract: Riboswitches are conserved regulatory RNA elements participating in various metabolic pathways. Recently, a novel RNA motif known as the folE RNA motif was discovered upstream of folE genes. It specifically senses tetrahydrofolate (THF) and is therefore termed THF-II riboswitch. To unravel the ligand recognition mechanism of this newly discovered riboswitch and decipher the underlying principles governing its tertiary folding, we determined both the free-form and bound-form THF-II riboswitch in the wild-type sequences. Combining structural information and isothermal titration calorimetry (ITC) binding assays on structure-based mutants, we successfully elucidated the significant long-range interactions governing the function of THF-II riboswitch and identified additional compounds, including alternative natural metabolites and potential lead compounds for drug discovery, that interact with THF-II riboswitch. Our structural research on the ligand recognition mechanism of the THF-II riboswitch not only paves the way for identification of compounds targeting riboswitches, but also facilitates the exploration of THF analogs in diverse biological contexts or for therapeutic applications.

PubMed: 38769061
DOI: 10.1093/nar/gkae377

Experimental method

X-RAY DIFFRACTION (1.98 Å)