7MLW

Burkholderia sp. TJI49 Guanidine-I riboswitch

7MLW の概要

• エントリーDOI: 10.2210/pdb7mlw/pdb
• 分子名称: Guanidine-I riboswitch, GUANIDINE, PHOSPHATE ION, ... (7 entities in total)
• 機能のキーワード: riboswitch, guanidine, potassium, ion, a-minor, rna
• 由来する生物種: Burkholderia sp. TJI49
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 42270.05

構造登録者

Trachman, R.J.,Ferre-D'Amare, A.R. (登録日: 2021-04-29, 公開日: 2022-01-12, 最終更新日: 2023-10-18)

主引用文献

Trachman 3rd, R.J.,Ferre-D'Amare, A.R.
An uncommon [K + (Mg 2+ ) 2 ] metal ion triad imparts stability and selectivity to the Guanidine-I riboswitch.
Rna, 27:1257-1264, 2021

PubMed Abstract: The widespread -I riboswitch class exemplifies divergent riboswitch evolution. To analyze how natural selection has diversified its versatile RNA fold, we determined the X-ray crystal structure of the -I subtype-1 (Guanidine-I) riboswitch aptamer domain. Differing from the previously reported structures of orthologs from and , our structure reveals a chelated K ion adjacent to two Mg ions in the guanidine-binding pocket. Thermal melting analysis shows that K chelation, which induces localized conformational changes in the binding pocket, improves guanidinium-RNA interactions. Analysis of ribosome structures suggests that the [K(Mg)] ion triad is uncommon. It is, however, reminiscent of metal ion clusters found in the active sites of ribozymes and DNA polymerases. Previous structural characterization of -I subtype-2 RNAs, which bind the effector ligands ppGpp and PRPP, indicate that in those paralogs, an adenine responsible for K chelation in the Guanidine-I riboswitch is replaced by a pyrimidine. This mutation results in a water molecule and Mg ion binding in place of the K ion. Thus, our structural analysis demonstrates how ion and solvent chelation tune divergent ligand specificity and affinity among -I riboswitches.

PubMed: 34257148
DOI: 10.1261/rna.078824.121

実験手法

X-RAY DIFFRACTION (2.7 Å)