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

  • Nat Struct Mol Biol. 2019 Jul;26(7):607-612. doi: 10.1038/s41594-019-0246-6.
Levon Halabelian  1 ,  Mani Ravichandran  1 ,  Yanjun Li  1 ,  Hong Zeng  1 ,  Anjana Rao  2  3  4  5 ,  L Aravind  6  7 ,  Cheryl H Arrowsmith  8  9  10
Affiliations
  • 1. Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.
  • 2. Division of Signaling and Gene Expression, La Jolla Institute for Immunology, La Jolla, CA, USA.
  • 3. Department of Pharmacology, University of San Diego, La Jolla, CA, USA.
  • 4. Moores Cancer Center, University of San Diego, La Jolla, CA, USA.
  • 5. Sanford Consortium for Regenerative Medicine, La Jolla, CA, USA.
  • 6. National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA.
  • 7. National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
  • 8. Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada. [email protected].
  • 9. Department of Medical Biophysics, University of Toronto, Toronto, Onatario, Canada. [email protected].
  • 10. Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada. [email protected].
PMID: 31235913 DOI: 10.1038/s41594-019-0246-6
Abstract

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.