4U35

Crystal Structures of RNA Duplexes Containing 2-thio-Uridine

4U35 の概要

• エントリーDOI: 10.2210/pdb4u35/pdb
• 関連するPDBエントリー: 4U34 4U37 4U38
• 分子名称: RNA (5'-R(*UP*AP*GP*CP*(SUR)P*CP*C-3'), RNA (5'-R(*GP*GP*UP*GP*CP*UP*A)-3') (3 entities in total)
• 機能のキーワード: rna, 2-thio-uridine
• 由来する生物種: synthetic construct; 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 4410.78

構造登録者

Sheng, J.,Larsen, A.,Heuberger, B.,Blain, J.C.,Szostak, J.W. (登録日: 2014-07-18, 公開日: 2014-08-13, 最終更新日: 2023-09-27)

主引用文献

Sheng, J.,Larsen, A.,Heuberger, B.D.,Blain, J.C.,Szostak, J.W.
Crystal Structure Studies of RNA Duplexes Containing s(2)U:A and s(2)U:U Base Pairs.
J.Am.Chem.Soc., 136:13916-13924, 2014

PubMed Abstract: Structural studies of modified nucleobases in RNA duplexes are critical for developing a full understanding of the stability and specificity of RNA base pairing. 2-Thio-uridine (s(2)U) is a modified nucleobase found in certain tRNAs. Thermodynamic studies have evaluated the effects of s(2)U on base pairing in RNA, where it has been shown to stabilize U:A pairs and destabilize U:G wobble pairs. Surprisingly, no high-resolution crystal structures of s(2)U-containing RNA duplexes have yet been reported. We present here two high-resolution crystal structures of heptamer RNA duplexes (5'-uagcs(2)Ucc-3' paired with 3'-aucgAgg-5' and with 3'-aucgUgg-5') containing s(2)U:A and s(2)U:U pairs, respectively. For comparison, we also present the structures of their native counterparts solved under identical conditions. We found that replacing O2 with S2 stabilizes the U:A base pair without any detectable structural perturbation. In contrast, an s(2)U:U base pair is strongly stabilized in one specific U:U pairing conformation out of four observed for the native U:U base pair. This s(2)U:U stabilization appears to be due at least in part to an unexpected sulfur-mediated hydrogen bond. This work provides additional insights into the effects of 2-thio-uridine on RNA base pairing.

PubMed: 25188906
DOI: 10.1021/ja508015a

実験手法

X-RAY DIFFRACTION (1.55 Å)