7TDB

Crystal structure of the E. coli thiM riboswitch in complex with thiamine bisphosphonate, manganese ions

Summary for 7TDB

• Entry DOI: 10.2210/pdb7tdb/pdb
• Descriptor: thiM riboswitch RNA (83-MER), [2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-1,3-thiazol-5-yl]ethoxy-oxidanyl-phosphoryl]methylphosphonic acid, MAGNESIUM ION, ... (5 entities in total)
• Functional Keywords: rna
• Biological source: Escherichia coli
• Total number of polymer chains: 1
• Total formula weight: 27594.89

Authors

Nuthanakanti, A.,Serganov, A. (deposition date: 2021-12-30, release date: 2022-02-16, Last modification date: 2023-10-18)

Primary citation

Zeller, M.J.,Nuthanakanti, A.,Li, K.,Aube, J.,Serganov, A.,Weeks, K.M.
Subsite Ligand Recognition and Cooperativity in the TPP Riboswitch: Implications for Fragment-Linking in RNA Ligand Discovery.
Acs Chem.Biol., 17:438-448, 2022

PubMed Abstract: RNA molecules can show high levels of cooperativity in their global folding and interactions with divalent ions. However, cooperativity at individual ligand-RNA interaction sites remains poorly understood. Here, we investigated the binding of thiamine and methylene diphosphonic acid (MDP, a soluble structural analogue of pyrophosphate) to the thiamine pyrophosphate riboswitch. These ligands each bind weakly at proximal subsites, with 10 μM and 1 mM affinities, respectively. The affinity of MDP moderately improves when thiamine or thiamine-like fragments are pre-bound to the RNA. Covalent linking of thiamine and MDP substantially increases riboswitch binding to a notable high affinity of 20 nM. Crystal structures and single-molecule correlated chemical probing revealed favorable induced fit effects upon binding of individual ligands and, unexpectedly, a substantial thermodynamically unfavorable RNA structural rearrangement upon binding of the linked thiamine-MDP ligand. Thus, linking of two ligands of modest affinity, accompanied by an unfavorable structural rearrangement, still yields a potent linked RNA-binding compound. Since complex ligands often bind riboswitches and other RNAs at proximal subsites, principles derived from this work inform and support fragment-linking strategies for identifying small molecules that interact with RNA specifically and with high affinity.

PubMed: 35060698
DOI: 10.1021/acschembio.1c00880

Experimental method

X-RAY DIFFRACTION (2.56 Å)