Extended Data Fig. 1: Crystal structure of TadA*8.20 in a complex with ssDNA containing the adenine transition-state analog 2-deoxy-8-azanebularine.
From: Improved cytosine base editors generated from TadA variants
a, The top panel depicts hydrolytic deamination of adenosine catalyzed by TadA. The bottom panel shows the hydration of the adenine analog, 2’-deoxy-8-azanebularine (d8Az), forming the transition-state analog that gets trapped in the active site by coordinating with zinc. b, The overall structure of the TadA*8.20 functional homodimer (chain A in dark green; chain B in light green) bound to ssDNA (yellow). c, The overall structure of TadA*8.20 monomer. The monomer (light green) contains five β-strands (β1 to β5) and six α-helices (α1 to α6) that fold into a single domain with a central five-stranded β-sheet surrounded by α-helices. The zinc ion is shown as a gray sphere. d, TadA*8.20 active site with ssDNA-d8Az transition-state analog bound. The catalytic zinc (gray) ion is coordinated to a histidine residue (H57), two cysteine residues (C87 and C90), and the d8Az transition-state analog (yellow). The hydrogen bonds are shown as gray dashed lines. e, The surface of TadA*8.20 dimer (dark and light green) bound to ssDNA (yellow), showing that ssDNA is bound in the active site deep cavity located at the protein dimer interface and interacts with residues from both monomers, including the substitutions I76Y, L84F, D108N, R152P, E155V, and I156F relative to the wild-type TadA. The substitutions at the protein surface are shown in orange (W23R, H36L, R51L, I76Y, and A106V), at the C-terminal in pink (S146C, D147R, R152P, Q154R, E155V, I156F, and K157N), and at the active site in cyan (P48A, V82S, L84F, and D108N). f, Interactions between ssDNA (yellow) and TadA*8.20 active site residues. The residues from chains A and B are shown in dark and light green, respectively. The protein surface, C-terminal, and active site substitutions are shown in orange (chain A), pink (chain B), and cyan (chain B), respectively. The zinc ion is shown in a gray sphere. The hydrogen bonds are shown as black dashed lines. A stereo view is shown in Supplementary Fig. 7.
