5Z9X

Arabidopsis SMALL RNA DEGRADING NUCLEASE 1 in complex with an RNA substrate

5Z9X の概要

• エントリーDOI: 10.2210/pdb5z9x/pdb
• 分子名称: Small RNA degrading nuclease 1, RNA (5'-R(P*GP*CP*CP*CP*AP*UP*UP*AP*G)-3'), SULFATE ION, ... (5 entities in total)
• 機能のキーワード: exonuclease, microrna turnover, protein-rna complex, plant protein, plant protein-rna complex, plant protein/rna
• 由来する生物種: Arabidopsis thaliana (Mouse-ear cress); 詳細
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 49830.75

構造登録者

Chen, J.,Liu, L.,You, C.,Gu, J.,Ruan, W.,Zhang, L.,Gan, J.,Cao, C.,Huang, Y.,Chen, X.,Ma, J. (登録日: 2018-02-05, 公開日: 2018-06-27, 最終更新日: 2024-04-03)

主引用文献

Chen, J.,Liu, L.,You, C.,Gu, J.,Ruan, W.,Zhang, L.,Gan, J.,Cao, C.,Huang, Y.,Chen, X.,Ma, J.
Structural and biochemical insights into small RNA 3' end trimming by Arabidopsis SDN1.
Nat Commun, 9:3585-3585, 2018

PubMed Abstract: A family of DEDDh 3'→5' exonucleases known as Small RNA Degrading Nucleases (SDNs) initiates the turnover of ARGONAUTE1 (AGO1)-bound microRNAs in Arabidopsis by trimming their 3' ends. Here, we report the crystal structure of Arabidopsis SDN1 (residues 2-300) in complex with a 9 nucleotide single-stranded RNA substrate, revealing that the DEDDh domain forms rigid interactions with the N-terminal domain and binds 4 nucleotides from the 3' end of the RNA via its catalytic pocket. Structural and biochemical results suggest that the SDN1 C-terminal domain adopts an RNA Recognition Motif (RRM) fold and is critical for substrate binding and enzymatic processivity of SDN1. In addition, SDN1 interacts with the AGO1 PAZ domain in an RNA-independent manner in vitro, enabling it to act on AGO1-bound microRNAs. These extensive structural and biochemical studies may shed light on a common 3' end trimming mechanism for 3'→5' exonucleases in the metabolism of small non-coding RNAs.

PubMed: 30181559
DOI: 10.1038/s41467-018-05942-7

実験手法

X-RAY DIFFRACTION (2.8 Å)