8E5E

Crystal structure of double-stranded DNA deaminase toxin DddA in complex with DNA with the target cytosine flipped into the active site

8E5E の概要

• エントリーDOI: 10.2210/pdb8e5e/pdb
• 分子名称: Double-stranded DNA deaminase toxin A, DNA (5'-D(*GP*TP*AP*CP*CP*GP*GP*AP*CP*GP*TP*TP*GP*C)-3'), DNA (5'-D(*GP*CP*AP*AP*CP*GP*TP*CP*CP*GP*GP*TP*AP*C)-3'), ... (6 entities in total)
• 機能のキーワード: toxin, dna binding, deaminase, toxin-dna complex, toxin/dna
• 由来する生物種: Burkholderia cenocepacia; 詳細
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 23338.50

構造登録者

Yin, L.,Shi, K.,Aihara, H. (登録日: 2022-08-21, 公開日: 2023-05-24, 最終更新日: 2024-09-18)

主引用文献

Yin, L.,Shi, K.,Aihara, H.
Structural basis of sequence-specific cytosine deamination by double-stranded DNA deaminase toxin DddA.
Nat.Struct.Mol.Biol., 30:1153-1159, 2023

PubMed Abstract: The interbacterial deaminase toxin DddA catalyzes cytosine-to-uracil conversion in double-stranded (ds) DNA and enables CRISPR-free mitochondrial base editing, but the molecular mechanisms underlying its unique substrate selectivity have remained elusive. Here, we report crystal structures of DddA bound to a dsDNA substrate containing the 5'-TC target motif. These structures show that DddA binds to the minor groove of a sharply bent dsDNA and engages the target cytosine extruded from the double helix. DddA Phe1375 intercalates in dsDNA and displaces the 5' (-1) thymine, which in turn replaces the target (0) cytosine and forms a noncanonical T-G base pair with the juxtaposed guanine. This tandem displacement mechanism allows DddA to locate a target cytosine without flipping it into the active site. Biochemical experiments demonstrate that DNA base mismatches enhance the DddA deaminase activity and relax its sequence selectivity. On the basis of the structural information, we further identified DddA mutants that exhibit attenuated activity or altered substrate preference. Our studies may help design new tools useful in genome editing or other applications.

PubMed: 37460895
DOI: 10.1038/s41594-023-01034-3

実験手法

X-RAY DIFFRACTION (2.62 Å)