AP-endonuclease 1 sculpts DNA through an anchoring tyrosine residue on the DNA intercalating loop.

Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Print Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE

Publication: 1992- : Oxford : Oxford University Press
Original Publication: London, Information Retrieval ltd.

DNA/*chemistry ; DNA-(Apurinic or Apyrimidinic Site) Lyase/*chemistry; Catalytic Domain ; DNA/metabolism ; DNA-(Apurinic or Apyrimidinic Site) Lyase/genetics ; DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism ; Humans ; Molecular Dynamics Simulation ; Mutation ; Nucleotide Motifs ; Protein Binding ; Tyrosine/chemistry ; Tyrosine/genetics

Base excision repair (BER) maintains genomic stability through the repair of DNA damage. Within BER, AP-endonuclease 1 (APE1) is a multifunctional enzyme that processes DNA intermediates through its backbone cleavage activity. To accomplish these repair activities, APE1 must recognize and accommodate several diverse DNA substrates. This is hypothesized to occur through a DNA sculpting mechanism where structural adjustments of the DNA substrate are imposed by the protein; however, how APE1 uniquely sculpts each substrate within a single rigid active site remains unclear. Here, we utilize structural and biochemical approaches to probe the DNA sculpting mechanism of APE1, specifically by characterizing a protein loop that intercalates the minor groove of the DNA (termed the intercalating loop). Pre-steady-state kinetics reveal a tyrosine residue within the intercalating loop (Y269) that is critical for AP-endonuclease activity. Using X-ray crystallography and molecular dynamics simulations, we determined the Y269 residue acts to anchor the intercalating loop on abasic DNA. Atomic force microscopy reveals the Y269 residue is required for proper DNA bending by APE1, providing evidence for the importance of this mechanism. We conclude that this previously unappreciated tyrosine residue is key to anchoring the intercalating loop and stabilizing the DNA in the APE1 active site.
(© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.)

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R01 GM105978 United States GM NIGMS NIH HHS; United States HHMI Howard Hughes Medical Institute; R01 ES029203 United States ES NIEHS NIH HHS; R01 ES019566 United States ES NIEHS NIH HHS; R01 ES028686 United States ES NIEHS NIH HHS

42HK56048U (Tyrosine)
9007-49-2 (DNA)
EC 4.2.99.18 (APEX1 protein, human)
EC 4.2.99.18 (DNA-(Apurinic or Apyrimidinic Site) Lyase)

Date Created: 20200617 Date Completed: 20200916 Latest Revision: 20240731

20250114

PMC7367167

10.1093/nar/gkaa496

32542366