Extended Data Fig. 2: Crystal structure of T_ADAC-1.17 in a complex with ssDNA containing the adenine transition-state analog 2-deoxy-8-azanebularine.

a, The overall structure of the T_ADAC-1.17 functional homodimer (chain A in dark blue; chain B in slate blue) with ssDNA (yellow) bound. The substitutions (T17A, A48G, S82T, and A142E) relative to TadA*8.20 are shown in cyan spheres. b, The overall structure of T_ADAC-1.17 monomer (slate blue) in a complex with ssDNA (yellow). The monomer 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. C and 5′ represent the C-terminus and 5′-end of the ssDNA, respectively. c, T_ADAC-1.17 active site with ssDNA-d8Az transition-state analog bound. The catalytic zinc ion (gray sphere) coordinates H57, C87, C90, and the d8Az transition-state analog (yellow). The T82 side chain (cyan) is near the catalytic E59 side chain (3.9-Å; cyan dashed line) and may play a role in deamination by donating/accepting a proton to/from E59. The residue A17 (cyan) is in α1-helix at the protein surface. The residue G48 (cyan) is in α2-helix at the substrate binding pocket. The H-bonds between the d8Az transition-state analog and protein residues are shown as gray dashed lines. d, The side chain of the E142, located in α5-helix, H-bonds (gray dashed line) to the R153 side chain, located in α6-helix, and helps stabilize the C-terminal α6-helix to position the F156 side chain to interact (cyan dashed lines) with the pyrimidine base of dT(8).