Metal ion mediated nucleobase recognition by the ZTP riboswitch
By J. Trausch, Joan G Marcano-Velázquez, M. M. Matyjasik, R. Batey. 2015
56 citations recorded by the source corpus.
SUMMARY The ZTP riboswitch is a widespread family of regulatory RNAs that upregulate de novo purine synthesis in response to increased intracellular levels of ZTP or ZMP (AICAR). As an important intermediate in purine biosynthesis, ZMP also serves as a proxy for the concentration of 10-formyltetrahydrofolate, a key component of one carbon metabolism. Here we report the structure of the ZTP riboswitch bound to ZMP at a resolution of 1.80 Å. The RNA contains two subdomains brought together through a long-range pseudoknot further stabilized through helix-helix packing. ZMP is bound at the subdomain interface of the RNA through a set of interactions with the ligand's base, ribose sugar and phosphate moieties. Unique to nucleobase recognition by RNAs, the Z base is inner sphere coordinated to a magnesium cation bound by two backbone phosphates. This interaction, along with steric hindrance by the backbone, imparts specificity over related analogs such as ATP/AMP.
Subfields: Molecular Biology
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In Molecular Biology
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Citations in the corpus
- Accurate RNA 3D structure prediction using a language model-based deep learning approach (2022, neutral): “Similar findings were also observed for the ZTP riboswitch 46 (Supplementary Fig.”
- RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme (2017, methodology): “RNA–protein docking was performed using a procedure that in the meantime has been automated and now is available via the NPDock web server (Tuszynska et al. 2015).”
- Structure and ligand binding of the glutamine-II riboswitch (2019, background): “Such domain exchange within a crystal lattice is not unusual in small RNA molecules, having been observed in the ZTP riboswitch (27).”
- FARFAR2: Improved de novo Rosetta prediction of complex global RNA folds (2020, unknown): “…2014); 5KPY (Porter et al., 2017); 4LCK (Zhang and Ferre´-D’Amare´, 2013); 5LYU (Martinez-Zapien et al., 2017); 4QLM (Ren and Patel, 2014); 4XW7 (Trausch et al., 2015); 5DDP (Ren et al., 2015); 5DDO (Ren et al., 2015); 5DI4 (Mir et al., 2015); 5K7C (Ren et al., 2016); 5TPY (Akiyama et al.,…”