9C63

High resolution structure of cytidine deaminase T6S toxin from Pseudomonas syringae

9C63 の概要

• エントリーDOI: 10.2210/pdb9c63/pdb
• 分子名称: SsdA, ZINC ION, PHOSPHATE ION, ... (6 entities in total)
• 機能のキーワード: toxin, dna binding, deaminase, toxin-dna complex
• 由来する生物種: Pseudomonas syringae
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 36595.29

構造登録者

Yin, L.,Shi, K.,Aihara, H. (登録日: 2024-06-07, 公開日: 2025-11-12)

主引用文献

Yin, L.,Chen, Y.,Shi, K.,Barreto Duran, E.,Harris, R.S.,Aihara, H.
Structural basis for sequence context-independent single-stranded DNA cytosine deamination by the bacterial toxin SsdA.
Nat Commun, 16:8841-8841, 2025

PubMed Abstract: DNA deaminase toxins are involved in interbacterial antagonism and the generation of genetic diversity in surviving bacterial populations. These enzymes have also been adopted as genome engineering tools. The single-stranded (ss)DNA deaminase SsdA is representative of the bacterial deaminase toxin family-2 (BaDTF2), and it deaminates ssDNA cytosines without a strong sequence context dependence, which contrasts with the AID/APOBEC family of sequence-selective ssDNA cytosine deaminases. Here we report the crystal structure of SsdA in complex with a ssDNA substrate. The structure reveals a unique mode of substrate binding, in which a cluster of aromatic residues engages ssDNA in a V-shaped conformation sharply bent across the target cytosine. The bases 5' or 3' to the target cytosine are stacked linearly and make mostly sequence non-specific protein contacts, thus explaining the broad substrate selectivity of SsdA. Unexpectedly, SsdA contains a β-amino acid isoaspartate, which is important for enzymatic activity and contributes to the stability of SsdA as a toxin. Structure-function studies helped to design SsdA mutants active in human cells, which could lead to future applications in genome engineering.

PubMed: 41044082
DOI: 10.1038/s41467-025-63943-9

実験手法

X-RAY DIFFRACTION (1.34 Å)