Fig. 5: Crystal structure of Waddlia VTD1.
a Crystal structure of Wc-VTD1 (teal) in covalent complex with Ub-PA (orange) in cartoon representation. The α9 helix is colored blue, β2 is pink and the P383F384 loop is depicted in yellow. b Structural superposition of apo WcVTD1 (yellow) and ubiquitin-bound Wc-VTD1 (teal). The RMSD is 0.54 Å over 205 residues. c Magnification of α9 interaction with S1 ubiquitin. Residues of α9 in Wc-VTD1 are shown as blue sticks and the hydrophobic interaction interface of ubiquitin as orange sticks. d Putative interactions between ubiquitin’s Ile44 patch (residues shown as orange sticks) with Wc-VTD1 through its α9 (blue), β2 (pink) and P383F384 loop (yellow). Mutated residues are shown as sticks. e Activity of wildtype Wc-VTD1 (WT) against K6-linked di-ubiquitin compared to the binding mutants F384A, A392G, L481A. f Reaction of Wc-VTD1 with the wildtype Ub (Ub-PA) and UbI44A activity-based probe after overnight incubation (18 h). Asterisk marks the shifted bands after reaction. g Interaction of Wc-VTD1 (teal) with ubiquitin’s C-terminus (orange). The C-terminus of ubiquitin is shown as orange sticks and the propargylamide bond is marked with an asterisk. The catalytic cysteine of Wc-VTD1 is colored yellow and E363 and N364 are shown as grey sticks. The electron density map highlights the flexible R74. h Activity of wildtype Wc-VTD1 (WT) against K6-linked di-ubiquitin compared to the catalytically inactive mutants C313A, D440A and H442A, and against binding mutants E363A and N364A. i) Activity of wildtype Wc-VTD1 (WT) against K6-linked di-ubiquitin compared to mutants of surface-exposed residues, potentially forming the S1´ site. Source data are provided as a Source Data file.
