Structural and biophysical studies of human E3 ligase Deltex 4

Deltex E3 ligases such as DTX1 and DTX2 are known to bind to ADP-ribosylated substrates and consequently ubiquitinate them. However, little is known about the role of the deltex E3 ligase DTX4 in substrate binding and ubiquitination. Here, we present the crystal structure of the DTX4 RING-DTC domains in complex with ADP-ribose to a final resolution of 2.8 Å and uncover a unique domain swap within the RING domain. Structural comparison with the closely related RING-DTC domains of DTX1 and DTX2 reveals similarities but also differences in the mode of ligand binding and the number and type of conserved residues. Biophysical assays to assess the strength of binding to nucleotide units of poly-ADP-ribose (PAR) demonstrate a preference for binding to ADP-ribose, strengthening existing evidence for PAR binding. Collectively, the structural and binding data offer insights into the active structure of DTX4 and its interaction with nucleotide units of PAR.