Fig. 6: Comparison of hMYDGF and human VNN1 base domain.

a Left: superposition of ordered residues (P35-A126, D133-A168) from the NMR structure of hMYDGF upon the crystal structure of the human VNN1 base domain (PDB 4CYF (https://www.rcsb.org/structure/4CYF)²⁸; cyan). 110 residues aligned with a Cα RMSD of 4.0 Å. The VNN1 base domain is flanked by a nitrilase domain at the N-terminus and a GPI anchor at the C-terminus (cyan arrows highlight the strands of the base domain that lead to these features). Right: stick representations of highly conserved residues (circled) shared by human VNN1 (cyan) and hMYDGF superimposed on the hMYDGF structure. b Multiple sequence alignment and consensus logo of hMYDGF, human VNN1 base domain, and Pfam seed sequences for MYDGF (Pfam: PF10572 (http://pfam.xfam.org/family/PF10572)) and vanin base domain (Pfam: PF19018 (http://pfam.xfam.org/family/PF19018)) families (82 sequences total). hMYDGF and the human VNN1 base domain are displayed as representative sequences, with hMYDGF sharing 15% sequence identity with the VNN1 base domain. Asterisks represent eight highly conserved residues among all sequences (black, ≥90% identity; gray, ≥85% identity), which align well in space between hMYDGF and the human VNN1 base domain as shown in a. c The VNN1 base domain (cyan) is connected to the nitrilase domain (blue) via a linker strand (pink) at its N-terminus and tethered to the plasma membrane by a GPI anchor at the C-terminus. An analogous model of hMYDGF (colored by residue conservation as in Fig. 5: blue, most conserved; orange, most variable) is presented in a similar orientation as the VNN1 base domain and engaging cKDELR2 (PDB 6I6H (https://www.rcsb.org/structure/6I6H)⁶; purple) from HADDOCK cluster 1 (Supplementary Fig. 4) in the Golgi via its C-terminal ERS with the remaining highly conserved residues on the opposite face. d. The 14 most-conserved MYDGF residues (Fig. 5, bin 9) that do not overlap with conserved residues shared with vanin base family members (asterisks in b) are highlighted as dark blue sticks. Note that aside from the C-terminal Glu-Leu residues of the ERS, these MYDGF-specific conserved residues reside in the loops on the face opposite to the ERS and surface of the cavity (red).