3SUH

Crystal structure of THF riboswitch, bound with 5-formyl-THF

3SUH の概要

• エントリーDOI: 10.2210/pdb3suh/pdb
• 関連するPDBエントリー: 3SUX 3SUY
• 分子名称: Riboswitch, SODIUM ION, N-[4-({[(6S)-2-amino-5-formyl-4-oxo-3,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)benzoyl]-L-glutamic acid, ... (4 entities in total)
• 機能のキーワード: three-way junction, pseudoknot, gene regulator, thf, rna
• 由来する生物種: Eubacterium siraeum V10Sc8a
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 33356.88

構造登録者

Huang, L.,Serganov, A.,Patel, D.J. (登録日: 2011-07-11, 公開日: 2011-09-14, 最終更新日: 2023-09-13)

主引用文献

Huang, L.,Ishibe-Murakami, S.,Patel, D.J.,Serganov, A.
Long-range pseudoknot interactions dictate the regulatory response in the tetrahydrofolate riboswitch.
Proc.Natl.Acad.Sci.USA, 108:14801-14806, 2011

PubMed Abstract: Tetrahydrofolate (THF), a biologically active form of the vitamin folate (B(9)), is an essential cofactor in one-carbon transfer reactions. In bacteria, expression of folate-related genes is controlled by feedback modulation in response to specific binding of THF and related compounds to a riboswitch. Here, we present the X-ray structures of the THF-sensing domain from the Eubacterium siraeum riboswitch in the ligand-bound and unbound states. The structure reveals an "inverted" three-way junctional architecture, most unusual for riboswitches, with the junction located far from the regulatory helix P1 and not directly participating in helix P1 formation. Instead, the three-way junction, stabilized by binding to the ligand, aligns the riboswitch stems for long-range tertiary pseudoknot interactions that contribute to the organization of helix P1 and therefore stipulate the regulatory response of the riboswitch. The pterin moiety of the ligand docks in a semiopen pocket adjacent to the junction, where it forms specific hydrogen bonds with two moderately conserved pyrimidines. The aminobenzoate moiety stacks on a guanine base, whereas the glutamate moiety does not appear to make strong interactions with the RNA. In contrast to other riboswitches, these findings demonstrate that the THF riboswitch uses a limited number of available determinants for ligand recognition. Given that modern antibiotics target folate metabolism, the THF riboswitch structure provides insights on mechanistic aspects of riboswitch function and may help in manipulating THF levels in pathogenic bacteria.

PubMed: 21873197
DOI: 10.1073/pnas.1111701108

実験手法

X-RAY DIFFRACTION (2.65 Å)