3UCZ

The c-di-GMP-I riboswitch bound to GpG

3UCZ の概要

• エントリーDOI: 10.2210/pdb3ucz/pdb
• 関連するPDBエントリー: 3UCU 3UD3 3UD4
• 分子名称: U1 small nuclear ribonucleoprotein A, RNA (92-MER), RNA (5'-R(*GP*G)-3'), ... (5 entities in total)
• 機能のキーワード: riboswitch, signaling protein-rna complex, signaling protein/rna
• 由来する生物種: Homo sapiens (human); 詳細
• 細胞内の位置: Nucleus: P09012
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 42001.46

構造登録者

Smith, K.D.,Strobel, S.A. (登録日: 2011-10-27, 公開日: 2012-01-04, 最終更新日: 2023-09-13)

主引用文献

Smith, K.D.,Lipchock, S.V.,Strobel, S.A.
Structural and biochemical characterization of linear dinucleotide analogues bound to the c-di-GMP-I aptamer.
Biochemistry, 51:425-432, 2012

PubMed Abstract: The cyclic dinucleotide c-di-GMP regulates lifestyle transitions in many bacteria, such as the change from a free motile state to a biofilm-forming community. Riboswitches that bind this second messenger are important downstream targets in this bacterial signaling pathway. The breakdown of c-di-GMP in the cell is accomplished enzymatically and results in the linear dinucleotide pGpG. The c-di-GMP-binding riboswitches must be able to discriminate between their cognate cyclic ligand and linear dinucleotides in order to be selective biological switches. It has been reported that the c-di-GMP-I riboswitch binds c-di-GMP 5 orders of magnitude better than the linear pGpG, but the cause of this large energetic difference in binding is unknown. Here we report binding data and crystal structures of several linear c-di-GMP analogues in complex with the c-di-GMP-I riboswitch. These data reveal the parameters for phosphate recognition and the structural basis of linear dinucleotide binding to the riboswitch. Additionally, the pH dependence of binding shows that exclusion of pGpG is not due to the additional negative charge on the ligand. These data reveal principles that, along with published work, will contribute to the design of c-di-GMP analogues with properties desirable for use as chemical tools and potential therapeutics.

PubMed: 22148472
DOI: 10.1021/bi2016662

実験手法

X-RAY DIFFRACTION (2.8 Å)