Extended Data Fig. 3: Cap2 is related to autophagy E1 and E2 proteins.

(a) Protein alignment of Cap2 from E. cloacae, Cap2 from V. cholerae, ATG10 from S. cerevisiae (4EBR⁷²), and ATG7 from S. cerevisiae (3T7H²⁴). Domains are indicated above the alignment with colors corresponding to Fig. 2. The secondary structure of Cap2 from E. cloacae is indicated in purple with alpha helices depicted as cylinders and beta sheets as arrows. The catalytic cysteines found in the E2 and E1 domains are highlighted in red. See Supplementary Table 5 for relevant accession numbers. (b) Domain schematic of E. cloacae Cap2 and S. cerevisiae ATG7, with approximate root-mean-squared distance (Cα r.m.s.d.) values for the linker/NTD and E1 domains noted. (c) Structures of E. cloacae Cap2 (left), compared to S. cerevisiae ATG7 (right; PDB ID 4GSK²²), with one protomer colored as in panel (a) and the dimer mate colored gray. For each protein, the E1 active-site cysteine residue (C548 for Cap2, C507 for ATG7) is shown as a sphere and labeled. (d) Structures of the E. cloacae Cap2 linker domain (left), compared to the S. cerevisiae ATG7 NTD (right; PDB ID 4GSK²²). ATG7 features a second subdomain (residues 147-268, shown in white) inserted into the loop separating β-strands 6 and 7 (labeled) where Cap2 has a partially disordered loop (residues 319–356). (e) Structure of the Cap2 E2 domain (active-site C109 shown as a sphere), compared to Kluyveromyces marxianus ATG10 (PDB ID 3VX7²³), S. cerevisiae ATG3 (PDB ID 2DYT⁷³), and Homo sapiens UBE2D2 (PDB ID 4DDG⁷⁴). Structural features not shared are shown in white. The active-site cysteine of each protein is shown as a sphere.