Metalloendopeptidase that acts selectively on DNA-binding proteins. DNA is needed to bring the protease and substrates together to enable proteolysis. Involved in the repair of toxic DNA-protein cross-links (DPCs) such as covalently trapped topoisomerase 1 (top1) adducts on DNA lesions or DPCs induced by reactive compounds such as formaldehyde. Involved in DNA damage response and processing of stalled or collapsed replication forks by removing the covalently trapped top1 from chromatin. DPC proteolysis enables the repair of the lesions via downstream DNA repair pathways. May be recruited to DPCs via the SUMOylation of substrate proteins at damaged DNA sites (By similarity). Binds to DNA. Interacts with pmt3/smt3. The SUMO interaction motif (SIM) is important for binding to pmt3/smt3 (SUMO). Belongs to the peptidase M3 family. WSS1-like metalloprotease (WLM) subfamily.