Fig. 2. Structure-based sequence alignment of OTP86^DYW.

The alignment compares OTP86^DYW with plant organellar DYW domains, hornwort putative U-to-C aminases^53,72, C-to-U deaminases from E. coli (EcCD, PDB-ID: 1AF2; ref. ⁴³), and Mus musculus (MmCD, PDB-ID: 2FR6; ref. ⁴⁴). The alignment was prepared by Chimera employing Clustal Omega and shaded with ALSCRIPT^73,74. Proteins are identified on the left of the aligned sequences with residues numbered (see Supplementary Table 2). Higher conservation is indicated by a darker background. Full conservation within DYW domains is indicated by dark blue background shading. Single-residue Cα r.m.s.d. values (calculated with CCP4i) between OTP86^DYW and OTP86^DYW★ (or structural changes upon activation) are displayed on the top of each alignment block as a colour gradient from white to pink (prepared with Python Matplotlib) and are quantified in the top-right box. The overall r.m.s.d. between the two structures was 1.99 Å, the gating domain residues 870–891 (β-finger) amounted to 2.98 Å. The numbering on top of each block refers to A. thaliana OTP86. Below the alignment blocks, secondary structure elements (α–α-helix, β-β-sheet) of OTP86^DYW are shown in slate for the deaminase domain, orange for the gating domain and red for the DYW motif. A dashed line or no line indicates residues missing from the structure or the expression construct, respectively. Green shading indicates residues coordinating the catalytic Zn1 ion; yellow shading indicates residues coordinating the Zn2 atom within the DYW motif and strand β7/helix α3; and purple shading indicates residues relevant for catalysis according to past studies. At, Arabidopsis thaliana; Pp, Physcomitrium patens; Aa, Anthoceros agrestis.