8E2P

Crystal structure of TadA*8.20 in a complex with ssDNA

Summary for 8E2P

• Entry DOI: 10.2210/pdb8e2p/pdb
• Descriptor: tRNA-specific adenosine deaminase 8.20, DNA (5'-D(P*GP*CP*TP*CP*GP*GP*CP*TP*(D8A)P*CP*GP*GP*A)-3'), ZINC ION, ... (4 entities in total)
• Functional Keywords: deaminase, ssdna, tada, dna binding protein, dna binding protein-dna complex, dna binding protein/dna
• Biological source: Escherichia coli; More
• Total number of polymer chains: 8
• Total formula weight: 91198.67

Authors

Feliciano, P.R.,Lee, S.J.,Ciaramella, G. (deposition date: 2022-08-15, release date: 2023-01-11, Last modification date: 2023-10-25)

Primary citation

Lam, D.K.,Feliciano, P.R.,Arif, A.,Bohnuud, T.,Fernandez, T.P.,Gehrke, J.M.,Grayson, P.,Lee, K.D.,Ortega, M.A.,Sawyer, C.,Schwaegerle, N.D.,Peraro, L.,Young, L.,Lee, S.J.,Ciaramella, G.,Gaudelli, N.M.
Improved cytosine base editors generated from TadA variants.
Nat.Biotechnol., 41:686-697, 2023

PubMed Abstract: Cytosine base editors (CBEs) enable programmable genomic C·G-to-T·A transition mutations and typically comprise a modified CRISPR-Cas enzyme, a naturally occurring cytidine deaminase, and an inhibitor of uracil repair. Previous studies have shown that CBEs utilizing naturally occurring cytidine deaminases may cause unguided, genome-wide cytosine deamination. While improved CBEs that decrease stochastic genome-wide off-targets have subsequently been reported, these editors can suffer from suboptimal on-target performance. Here, we report the generation and characterization of CBEs that use engineered variants of TadA (CBE-T) that enable high on-target C·G to T·A across a sequence-diverse set of genomic loci, demonstrate robust activity in primary cells and cause no detectable elevation in genome-wide mutation. Additionally, we report cytosine and adenine base editors (CABEs) catalyzing both A-to-I and C-to-U editing (CABE-Ts). Together with ABEs, CBE-Ts and CABE-Ts enable the programmable installation of all transition mutations using laboratory-evolved TadA variants with improved properties relative to previously reported CBEs.

PubMed: 36624149
DOI: 10.1038/s41587-022-01611-9

Experimental method

X-RAY DIFFRACTION (2.72 Å)