Figure - PMC

Skip to main content

An official website of the United States government

Here's how you know

Here's how you know

Official websites use .gov
A .gov website belongs to an official government organization in the United States.

Secure .gov websites use HTTPS
A lock ( ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

View full-text article in PMC

. 2023 Jan 9;41(5):686–697. doi: 10.1038/s41587-022-01611-9

Search in PMC
Search in PubMed
View in NLM Catalog
Add to search

© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

PMC Copyright notice

Extended Data Fig. 4 — a, Overall structure of the T_ADAC-1.19 functional homodimer (dark and light pink). E27G and I49N substitutions relative to TadA*8.20 are shown in orange spheres. Zinc ion is shown as a gray sphere. b, Overall structure of T_ADAC-1.19 monomer. C represents C-terminus. c, T_ADAC-1.19 active site with water (red sphere) bound to the zinc ion. H57, C87, and C90 coordinate with the zinc ion. The water molecule H-bonds (dashed lines) to the catalytic residue E59. d–h, Structural comparisons between T_ADAC-1.19 and TadA*8.20 structures. (d) Superposition between substrate-free T_ADAC-1.19 (pink) and ssDNA-bound TadA*8.20 (green, yellow) monomers, showing high structural similarity (RMSD of ~0.9-Å for all of the Cα atoms). The main structural differences are in α1-helix, the loop between α1 and β1, and C-terminal α5- and α6- helices. (e) TadA*8.20 has E27 side chain H-bonding (black dashed lines) to the main chains of A48, I49, and G50, and E27G substitution removes these interactions. To compensate for these critical contacts, T_ADAC1.19 places E25 at a similar position to the formerly occupied by E27 in TadA*8.20 to make the same H-bonds (orange dashed lines) with A48, I49, and G50. E25 displacement shortens α1-helix, and the loop between α1 and β1 (orange), containing E27G substitution, is extended and adapts into a different conformation compared to TadA*8.20 (d, f, and g). This results in partial unfolding of α5-helix to prevent steric clash with this loop conformation and complete unfolding of α6-helix (d and g). These structural changes alter the shape of the T_ADAC-T1.19 active site cavity (h), affecting substrate binding in the active site (Fig. 2b). R26 present in T_ADAC-T1.19-loop (orange) would make close contacts (cyan dashed lines) with dC(10), adjacent to the target base d8Az(9), and dG(11) of TadA*8.20-ssDNA (g). I49N substitution positions the N49 side chain far from the ssDNA backbone (~9-Å from dG(11); cyan dashed lines) (f), suggesting that a residue with a longer positively charged side chain like lysine would create additional contacts with the ssDNA, as observed in the T_ADAC-T1.14 structure (Extended Data Fig. 3e).