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

Area of Science:

• Molecular Biology
• Genetics
• Structural Biology

Background:

• Embryonic stem cell-specific 5-hydroxymethylcytosine-binding protein (HMCES) is crucial for preventing genome instability.
• HMCES functions by cross-linking to abasic sites in single-stranded DNA at stalled replication forks.

Purpose of the Study:

• To determine the structural basis of HMCES interaction with DNA damage.
• To elucidate the mechanism of HMCES-mediated DNA cross-linking.

Main Methods:

• X-ray crystallography
• Analysis of protein-DNA complexes
• Structural biology techniques

Main Results:

• Crystal structures of the human HMCES SOS response-associated peptidase (SRAP) domain complexed with DNA damage substrates were determined.
• The structures revealed HMCES cross-linked to an abasic site within a 3' overhang DNA.
• A novel thiazolidine covalent interaction between the DNA abasic site and conserved Cys2 of HMCES was identified.
• Two independent duplex DNA interaction sites within the SRAP domain were characterized.
• The SRAP domain demonstrated interaction capabilities with diverse DNA structures, including 5' and 3' overhangs and gapped DNA.

Conclusions:

• The HMCES SRAP domain exhibits versatile DNA-binding capabilities, accommodating various single- and double-stranded DNA structures at damage sites.
• The identified covalent cross-link and interaction sites provide critical insights into HMCES's role in maintaining genome integrity.