9L55

Plastid Localized Exonuclease 1 (D249A) complexed with DNA

9L55 の概要

• エントリーDOI: 10.2210/pdb9l55/pdb
• 分子名称: 5'-3' exonuclease family protein, DNA (5'-D(P*TP*AP*CP*CP*TP*CP*AP*CP*AP*CP*CP*AP*CP*TP*TP*AP*AP*T)-3'), DNA (5'-D(P*AP*TP*TP*AP*AP*GP*TP*GP*GP*T)-3'), ... (6 entities in total)
• 機能のキーワード: exonuclease, plant protein/dna, plant protein-dna complex
• 由来する生物種: Zea mays; 詳細
• タンパク質・核酸の鎖数: 5
• 化学式量合計: 84477.56

構造登録者

Shi, G.,Zhang, Y. (登録日: 2024-12-22, 公開日: 2025-07-16, 最終更新日: 2025-08-06)

主引用文献

Huang, X.,Shi, G.,Xiao, Q.,Feng, J.,Huang, Y.,Shi, H.,Wang, Q.,Su, Y.,Wang, J.,Wu, X.,Cao, Y.,Wang, H.,Wang, W.,Zhang, Y.,Wu, Y.
PEN1 catalyses RNA primer removal during plastid DNA replication in maize.
Nat.Plants, 11:1325-1338, 2025

PubMed Abstract: The plastid DNA (ptDNA) replication is initiated by primases, which synthesize RNA primers; following the synthesis of DNA fragments, primers must be removed before ligation. However, the enzymes and mechanisms underlying this process are poorly understood. Here we cloned a gene from maize that encodes a plastid-localized and Mn-dependent 5'-3' exonuclease (designated PEN1) responsible for this process. The pen1 seeds show development and filling defects that intensify across generations. PEN1 cleaves the RNA primers, allowing for the complete excision of ribonucleotides. We reconstituted the plastid RNA primer removal processes in vitro. We also determined the crystal structure of the PEN1-dsDNA binary complex and explained the structural mechanism of the 5' to 3' exonuclease activity. Mutation of Pen1 resulted in the accumulation of ptDNA breaks, thereby compromising plastid function. These studies fill a critical gap that has long existed in the understanding of ptDNA replication.

PubMed: 40562815
DOI: 10.1038/s41477-025-02027-4

実験手法

X-RAY DIFFRACTION (2.87 Å)