9C64
Cytidine deaminase T6S toxin from Pseudomonas syringae complexed with substrate DNA
Summary for 9C64
| Entry DOI | 10.2210/pdb9c64/pdb |
| Descriptor | SsdA, DNA (5'-D(*AP*AP*AP*AP*AP*AP*TP*CP*GP*AP*AP*AP*AP*AP*A)-3'), ZINC ION, ... (5 entities in total) |
| Functional Keywords | toxin, dna binding, deaminase, toxin-dna complex, toxin/dna |
| Biological source | Pseudomonas syringae More |
| Total number of polymer chains | 4 |
| Total formula weight | 45693.64 |
| Authors | |
| Primary citation | 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 Cited by 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: 41044082DOI: 10.1038/s41467-025-63943-9 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.94 Å) |
Structure validation
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