biostudies-literatureHalabelian LNCRR NIH HHSNIAID NIH HHSNCI NIH HHSWellcome TrustNIGMS NIH HHSNIH HHS607-612https://www.ebi.ac.uk/biostudies/studies/S-EPMC6609482biostudies-literatureUnknown26(7)Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein (HMCES) can covalently cross-link to abasic sites in single-stranded DNA at stalled replication forks to prevent genome instability. Here, we report crystal structures of the human HMCES SOS response-associated peptidase (SRAP) domain in complex with DNA-damage substrates, including HMCES cross-linked 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 cross-link structure provides structural insights into a novel thiazolidine covalent interaction between the DNA abasic site and conserved Cys 2 of HMCES. Collectively, our structures demonstrate the capacity for the SRAP domain to interact with a 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.Nature structural & molecular biologyStructural basis of HMCES interactions with abasic DNA and multivalent substrate recognition.PMC6609482R35 CA210043R37 CA042471S10 RR029205R01 AI040127P41 GM103403R01 CA151535S10 OD021832Rao ALi YHalabelian LArrowsmith CHRavichandran MZeng HAravind LfalseStructural basis of HMCES interactions with abasic DNA and multivalent substrate recognition.Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein (HMCES) can covalently cross-link to abasic sites in single-stranded DNA at stalled replication forks to prevent genome instability. Here, we report crystal structures of the human HMCES SOS response-associated peptidase (SRAP) domain in complex with DNA-damage substrates, including HMCES cross-linked 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 cross-link structure provides structural insights into a novel thiazolidine covalent interaction between the DNA abasic site and conserved Cys 2 of HMCES. Collectively, our structures demonstrate the capacity for the SRAP domain to interact with a 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.2019-01-01T00:00:00Z2019 Jul2024-11-13T06:49:17.538Z2020-05-22T00:07:24ZS-EPMC66094823123591310.1038/s41594-019-0246-6