4DRF

Crystal Structure of Bacterial Pnkp-C/Hen1-N Heterodimer

4DRF の概要

• エントリーDOI: 10.2210/pdb4drf/pdb
• 関連するPDBエントリー: 4DQZ
• 分子名称: Metallophosphoesterase, Methyltransferase type 12, GLYCEROL, ... (4 entities in total)
• 機能のキーワード: rna repair, rna ligase, ligase-activating, protein binding, transferase
• 由来する生物種: Clostridium thermocellum; 詳細
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 150330.90

構造登録者

Huang, R.H.,Wang, P. (登録日: 2012-02-17, 公開日: 2012-08-01, 最終更新日: 2024-02-28)

主引用文献

Wang, P.,Chan, C.M.,Christensen, D.,Zhang, C.,Selvadurai, K.,Huang, R.H.
Molecular basis of bacterial protein Hen1 activating the ligase activity of bacterial protein Pnkp for RNA repair.
Proc.Natl.Acad.Sci.USA, 109:13248-13253, 2012

PubMed Abstract: Ribotoxins cleave essential RNAs for cell killing in vivo, and the bacterial polynucleotide kinase-phosphatase (Pnkp)/hua enhancer 1 (Hen1) complex has been shown to repair ribotoxin-cleaved RNAs in vitro. Bacterial Pnkp/Hen1 is distinguished from other RNA repair systems by performing 3'-terminal 2'-O-methylation during RNA repair, which prevents the repaired RNA from repeated cleavage at the same site. To ensure the opportunity of 2'-O-methylation by bacterial Hen1 during RNA repair and, therefore, maintain the quality of the repaired RNA, Pnkp/Hen1 has evolved to require the participation of Hen1 in RNA ligation, because Pnkp alone is unable to carry out the reaction despite possessing all signature motifs of an RNA ligase. However, the precise role of Hen1 in RNA ligation is unknown. Here, we present the crystal structure of an active RNA ligase consisting of the C-terminal half of Pnkp (Pnkp-C) and the N-terminal half of Hen1 (Hen1-N) from Clostridium thermocellum. The structure reveals that the N-terminal domain of Clostridium thermocellum (Cth) Hen1, shaped like a left hand, grabs the flexible insertion module of CthPnkp and locks its conformation via further interaction with the C-terminal addition module of CthPnkp. Formation of the CthPnkp-C/Hen1-N heterodimer creates a ligation pocket with a width for two strands of RNA, depth for two nucleotides, and the adenosine monophosphate (AMP)-binding pocket at the bottom. The structure, combined with functional analyses, provides insight into the mechanism of how Hen1 activates the RNA ligase activity of Pnkp for RNA repair.

PubMed: 22847431
DOI: 10.1073/pnas.1209805109

実験手法

X-RAY DIFFRACTION (2.6 Å)