Fig. 3: Crystal structure of a Helitron-encoded VTD.
a Crystal structure of DrT1-VTD2 in cartoon representation. The catalytic triad and residues potentially important for ubiquitin interaction are shown as sticks. The unstructured loop is coloured purple. b Structural superposition of DrT1-VTD2 (blue) with M48 (PDB: 2J7Q, green). The RMSD is 2.5 Å for 192 Cα atoms. c Active site architecture of DrT1-VTD2 (green sticks) compared to M48 (PDB: 2J7Q, purple sticks). d Structural superposition of DrT1-VTD2 (blue) with AvrPphB (PDB: 1UKF, pink). The RMSD is 5.0 Å over 160 residues. e Active site architecture of DrT1-VTD2 (green sticks) compared to AvrPphB (PDB: 1UKF, purple sticks). f Activity of wildtype DrT1-VTD2 (WT) against K48-linked di-ubiquitin, compared to the catalytically inactive mutants C322A, D451A and H453A. g Activity of 5 nM wildtype DrT1-VTD2 (WT, black) against Ubiquitin-AMC, compared to 5 nM of the catalytically inactive mutants C322A (red), D451A (blue) and H453A (yellow). The RFU values are the means of triplicates. h Activity of 5 nM wildtype DrT1-VTD2 (WT, black) against Ubiquitin-AMC compared to 5 nM of the binding mutants D376A (green), E377A (red) and Δhairpin (blue). The RFU values are the means of triplicates. i Activity of wildtype DrT1-VTD2 (WT) against K48-linked di-ubiquitin compared to the binding mutants Δhairpin, F398A, P405A, A406G, L407A, D376A and E377A. j Activity of wildtype DrT1-VTD2 (WT) or the quadruple mutant DrT1-VTD24mut (F398A, P405A, A406G and L407A) against K48-linked di-ubiquitin. k Reaction of DrT1-VTD2 or M48 with the wildtype Ub (Ub-PA) and UbI44A activity-based probe after overnight incubation (18 h). Asterisks mark the shifted bands after reaction. Source data are provided as a Source Data file.
