7ELP

Crystal structure of xanthine riboswitch with xanthine, iridium hexammine soak

7ELP の概要

• エントリーDOI: 10.2210/pdb7elp/pdb
• 分子名称: NMT1_Ir(46-MER), GUANOSINE-5'-TRIPHOSPHATE, IRIDIUM ION, ... (6 entities in total)
• 機能のキーワード: rna, riboswitch, xanthine
• 由来する生物種: Ideonella sp. B508-1
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 31433.61

構造登録者

Xu, X.C.,Ren, A.M. (登録日: 2021-04-12, 公開日: 2021-06-30, 最終更新日: 2024-05-29)

主引用文献

Xu, X.,Egger, M.,Chen, H.,Bartosik, K.,Micura, R.,Ren, A.
Insights into xanthine riboswitch structure and metal ion-mediated ligand recognition.
Nucleic Acids Res., 49:7139-7153, 2021

PubMed Abstract: Riboswitches are conserved functional domains in mRNA that mostly exist in bacteria. They regulate gene expression in response to varying concentrations of metabolites or metal ions. Recently, the NMT1 RNA motif has been identified to selectively bind xanthine and uric acid, respectively, both are involved in the metabolic pathway of purine degradation. Here, we report a crystal structure of this RNA bound to xanthine. Overall, the riboswitch exhibits a rod-like, continuously stacked fold composed of three stems and two internal junctions. The binding-pocket is determined by the highly conserved junctional sequence J1 between stem P1 and P2a, and engages a long-distance Watson-Crick base pair to junction J2. Xanthine inserts between a G-U pair from the major groove side and is sandwiched between base triples. Strikingly, a Mg2+ ion is inner-sphere coordinated to O6 of xanthine and a non-bridging oxygen of a backbone phosphate. Two further hydrated Mg2+ ions participate in extensive interactions between xanthine and the pocket. Our structure model is verified by ligand binding analysis to selected riboswitch mutants using isothermal titration calorimetry, and by fluorescence spectroscopic analysis of RNA folding using 2-aminopurine-modified variants. Together, our study highlights the principles of metal ion-mediated ligand recognition by the xanthine riboswitch.

PubMed: 34125892
DOI: 10.1093/nar/gkab486

実験手法

X-RAY DIFFRACTION (2.79 Å)