2MN0

D loop of tRNA(Met)

2MN0 の概要

• エントリーDOI: 10.2210/pdb2mn0/pdb
• NMR情報: BMRB: 19873
• 分子名称: 5'-R(*GP*GP*AP*GP*AP*GP*(H2U)P*GP*GP*AP*AP*CP*UP*CP*C)-3' (1 entity in total)
• 機能のキーワード: trna, d arm, h2u, rna
• 由来する生物種: Schizosaccharomyces pombe
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 4872.99

構造登録者

Lescrinier, E.,Dyubankova, N.,Herdewijn, P. (登録日: 2014-03-25, 公開日: 2015-04-15, 最終更新日: 2024-05-15)

主引用文献

Dyubankova, N.,Sochacka, E.,Kraszewska, K.,Nawrot, B.,Herdewijn, P.,Lescrinier, E.
Contribution of dihydrouridine in folding of the D-arm in tRNA.
Org.Biomol.Chem., 13:4960-4966, 2015

PubMed Abstract: Posttranscriptional modifications of transfer RNAs (tRNAs) are proven to be critical for all core aspects of tRNA function. While the majority of tRNA modifications were discovered in the 1970s, their contribution in tRNA folding, stability, and decoding often remains elusive. In this work an NMR study was performed to obtain more insight in the role of the dihydrouridine (D) modification in the D-arm of tRNAi(Met) from S. pombe. While the unmodified oligonucleotide adopted several undefined conformations that interconvert in solution, the presence of a D nucleoside triggered folding into a hairpin with a stable stem and flexible loop region. Apparently the D modification is required in the studied sequence to fold into a stable hairpin. Therefore we conclude that D contributes to the correct folding and stability of D-arm in tRNA. In contrast to what is generally assumed for nucleic acids, the sharp 'imino' signal for the D nucleobase at 10 ppm in 90% H2O is not indicative for the presence of a stable hydrogen bond. The strong increase in pKa upon loss of the aromatic character in the modified nucleobase slows down the exchange of its 'imino' proton significantly, allowing its observation even in an isolated D nucleoside in 90% H2O in acidic to neutral conditions.

PubMed: 25815904
DOI: 10.1039/c5ob00164a

実験手法

SOLUTION NMR