9JGM

The Escherichia coli yybp riboswitch as a tandem riboswitch regulated by Mn2+ and pH

Summary for 9JGM

• Entry DOI: 10.2210/pdb9jgm/pdb
• Descriptor: yybP riboswitch, MAGNESIUM ION, MANGANESE (II) ION (3 entities in total)
• Functional Keywords: yybp, riboswitch, conformational dynamics, rna
• Biological source: Escherichia coli K-12
• Total number of polymer chains: 4
• Total formula weight: 136468.02

Authors

Xiao, W.W.,Liu, G.F.,Chen, T.,Zhang, Y.L.,Ke, A.L.,Cai, R.J.,Lu, C.R. (deposition date: 2024-09-08, release date: 2025-06-04)

Primary citation

Xiao, W.,Liu, G.,Chen, T.,Zhang, Y.,Ke, A.,Cai, R.,Lu, C.
Escherichia coli yybP-ykoY Riboswitch as a Tandem Riboswitch Regulated by Mn 2+ and pH.
Acs Chem.Biol., 20:1010-1019, 2025

PubMed Abstract: The riboswitch regulates and gene expression on the translation level. It contains two tandem domains regulated by Mn and pH. This study investigates the tertiary structure and conformational dynamics of the riboswitch using a combination of crystallography, small-angle X-ray scattering (SAXS), and chemical probing. Our crystal structure of the aptamer domain at 3.8 Å reveals that the riboswitch aptamer domain forms a coaxial superhelix containing three helices connected by a three-way junction (3WJ), with L1 and L3 creating a pocket-like structure that binds Mg and Mn. SHAPE probing and SAXS show that the riboswitch maintains a consistent conformation across pH conditions without Mn but exhibits significant conformational changes under alkaline conditions when Mn is present. These findings align with our proposed model, where Mn binding induces a transition from an "OFF" to an "ON" state in alkaline conditions, while the Mn remains bound to the aptamer independent of pH. This regulatory mechanism allows for more sophisticated control of gene expression, providing a finely tuned adaptive response to environmental changes.

PubMed: 40252020
DOI: 10.1021/acschembio.4c00715

Experimental method

X-RAY DIFFRACTION (3.73 Å)