Structural basis of HMCES interactions with abasic DNA and multivalent substrate recognition

HMCES can covalently crosslink to abasic sites in single-stranded DNA at stalled replication forks to prevent genome instability. Here, we report crystal structures of the Human HMCES SRAP domain in complex with DNA-damage substrates, including HMCES crosslinked with an abasic site within a 3’ overhang DNA. HMCES interacts with both single-strand and duplex segments of DNA, with two independent duplex DNA interaction sites identified in the SRAP domain. The HMCES DNA-protein crosslink structure provides structural insights into a novel thiazolidine covalent interaction between the DNA abasic site and conserved Cys2 of HMCES. Collectively, our structures demonstrate the capacity for the SRAP domain to interact with variety of single-strand and double-strand containing DNA structures found in DNA-damage sites including 5’ and 3’ overhang DNAs and gapped DNAs with short single-strand segments.