Molecular basis for discrimination of cGAMP linkage isomers by a c-di-GMP-II riboswitch variant
- 1Department of Cardiology of The Second Affiliated Hospital and Life Sciences Institute and School of Medicine, Zhejiang University, Hangzhou 310058, China
- 2Structural Biology Program, Memorial Sloan-Kettering Center, New York, NY 10065
Abstract
Riboswitches are noncoding RNA regulatory motifs predominantly found in bacteria. Signaling molecules such as c-di-GMP, c-di-AMP, and 3′,3′-cGAMP have been reported to be recognized by riboswitches. In contrast, 2′,3′-cGAMP functions as a second messenger in mammalian cells, yet its interaction with RNA molecules remains unclear. Here, we report the crystal structures of a c-di-GMP-II riboswitch variant, c-di-GMP-II-Bh, bound to 2′,3′-cGAMP and 3′,3′-cGAMP. Both complexes adopt a similar overall RNA scaffold with an identical binding pocket composition. However, the ligand bases adopt inverted orientations in the binding pocket, resulting in distinct interaction patterns with residues A64 and G68 and differences in base-pair stacking against the phosphodiester backbone. Structural comparison together with ligand-binding assays of structure-guided mutants using isothermal titration calorimetry reveals the molecular principles by which an RNA riboswitch discriminates among cyclic dinucleotide linkage isomers, highlighting the remarkable sensitivity of RNA binding pockets to subtle ligand structural variations and provides a mechanistic framework for understanding ligand specificity in RNA–small molecule recognition.
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BibTeX
@article{xu2026molecular,
title = {{Molecular basis for discrimination of cGAMP linkage isomers by a c-di-GMP-II riboswitch variant}},
author = {Xiaochen Xu and Wang Cheng and Huiqin You and Zejia Hu and Xinyue Bao and Hongcheng Li and Jinzhu Zhang and Dinshaw J. Patel and Aiming Ren},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
year = {2026},
month = oct,
doi = {10.1073/pnas.2621568123},
url = {https://doi.org/10.1073/pnas.2621568123},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - Molecular basis for discrimination of cGAMP linkage isomers by a c-di-GMP-II riboswitch variant
AU - Xiaochen Xu
AU - Wang Cheng
AU - Huiqin You
AU - Zejia Hu
AU - Xinyue Bao
AU - Hongcheng Li
AU - Jinzhu Zhang
AU - Dinshaw J. Patel
AU - Aiming Ren
PY - 2026
DA - 2026/10/20
JO - Proceedings of the National Academy of Sciences of the United States of America
DO - 10.1073/pnas.2621568123
UR - https://doi.org/10.1073/pnas.2621568123
AB - Riboswitches are noncoding RNA regulatory motifs predominantly found in bacteria. Signaling molecules such as c-di-GMP, c-di-AMP, and 3′,3′-cGAMP have been reported to be recognized by riboswitches. In contrast, 2′,3′-cGAMP functions as a second messenger in mammalian cells, yet its interaction with RNA molecules remains unclear. Here, we report the crystal structures of a c-di-GMP-II riboswitch variant, c-di-GMP-II-Bh, bound to 2′,3′-cGAMP and 3′,3′-cGAMP. Both complexes adopt a similar overall RNA scaffold with an identical binding pocket composition. However, the ligand bases adopt inverted orientations in the binding pocket, resulting in distinct interaction patterns with residues A64 and G68 and differences in base-pair stacking against the phosphodiester backbone. Structural comparison together with ligand-binding assays of structure-guided mutants using isothermal titration calorimetry reveals the molecular principles by which an RNA riboswitch discriminates among cyclic dinucleotide linkage isomers, highlighting the remarkable sensitivity of RNA binding pockets to subtle ligand structural variations and provides a mechanistic framework for understanding ligand specificity in RNA–small molecule recognition.
SN - 0027-8424
SN - 1091-6490
ER -