3B0P

tRNA-dihydrouridine synthase from Thermus thermophilus

3B0P の概要

• エントリーDOI: 10.2210/pdb3b0p/pdb
• 関連するPDBエントリー: 3B0U 3B0V
• 分子名称: tRNA-dihydrouridine synthase, FLAVIN MONONUCLEOTIDE (3 entities in total)
• 機能のキーワード: tim barrel, oxidoreductase
• 由来する生物種: Thermus thermophilus
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 80128.23

構造登録者

Yu, F.,Tanaka, Y.,Yamashita, K.,Nakamura, A.,Yao, M.,Tanaka, I. (登録日: 2011-06-12, 公開日: 2011-12-14, 最終更新日: 2024-03-13)

主引用文献

Yu, F.,Tanaka, Y.,Yamashita, K.,Suzuki, T.,Nakamura, A.,Hirano, N.,Suzuki, T.,Yao, M.,Tanaka, I.
Molecular basis of dihydrouridine formation on tRNA
Proc.Natl.Acad.Sci.USA, 108:19593-19598, 2011

PubMed Abstract: Dihydrouridine (D) is a highly conserved modified base found in tRNAs from all domains of life. Dihydrouridine synthase (Dus) catalyzes the D formation of tRNA through reduction of uracil base with flavin mononucleotide (FMN) as a cofactor. Here, we report the crystal structures of Thermus thermophilus Dus (TthDus), which is responsible for D formation at positions 20 and 20a, in complex with tRNA and with a short fragment of tRNA (D-loop). Dus interacts extensively with the D-arm and recognizes the elbow region composed of the kissing loop interaction between T- and D-loops in tRNA, pulling U20 into the catalytic center for reduction. Although distortion of the D-loop structure was observed upon binding of Dus to tRNA, the canonical D-loop/T-loop interaction was maintained. These results were consistent with the observation that Dus preferentially recognizes modified rather than unmodified tRNAs, indicating that Dus introduces D20 by monitoring the complete L-shaped structure of tRNAs. In the active site, U20 is stacked on the isoalloxazine ring of FMN, and C5 of the U20 uracil ring is covalently cross linked to the thiol group of Cys93, implying a catalytic mechanism of D20 formation. In addition, the involvement of a cofactor molecule in uracil ring recognition was proposed. Based on a series of mutation analyses, we propose a molecular basis of tRNA recognition and D formation catalyzed by Dus.

PubMed: 22123979
DOI: 10.1073/pnas.1112352108

実験手法

X-RAY DIFFRACTION (1.7 Å)