Structure and identification of ADP-ribose recognition motifs of APLF and role in the DNA damage response.
Poly(ADP-ribosyl)ation by poly(ADP-ribose) polymerases regulates the interaction of many DNA damage and repair factors with sites of DNA strand lesions. The interaction of these factors with poly(ADP-ribose) (PAR) is mediated by specific domains, including the recently identified PAR-binding zinc finger (PBZ) domain. However, the mechanism governing these interactions is unclear. To better understand the PBZ-PAR interaction, we performed a detailed examination of the representative PBZ-containing protein involved in the DNA damage response, aprataxin polynucleotide-kinase-like factor (APLF), which possesses two tandem PBZ domains. Here we present structural and biochemical studies that identify Y381/Y386 and Y423/Y428 residues in the conserved C(M/P)Y and CYR motifs within each APLF PBZ domain that are critical for the interaction with the adenine ring of ADP-ribose. Basic residues (R387 and R429 in the first and second PBZ domains, respectively) coordinate additional interactions with the phosphate backbone of ADP-ribose, suggesting that APLF binds to multiple ADP-ribose residues along PAR polymers. These C(M/P)Y and CYR motifs form a basic/hydrophobic pocket within a variant zinc finger structure and are required for APLF recruitment to sites of DNA damage in vivo.
Li
Guang-Yao
GY
Ontario Cancer Institute, 610 University Avenue, Toronto, ON, Canada M5G 2M9.
McCulloch
Richard D
RD
Fenton
Amanda L
AL
Cheung
Melissa
M
Meng
Li
L
Ikura
Mitsuhiko
M
Koch
C Anne
CA
D000246:Adenosine Diphosphate Ribose / Q000378:metabolism*; D000595:Amino Acid Sequence; D004249:DNA Damage; D004260:DNA Repair / Q000235:genetics*; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009711:Nucleotides / Q000378:metabolism; D010750:Phosphoproteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D000075223:Poly-ADP-Ribose Binding Proteins; D011487:Protein Conformation; D016415:Sequence Alignment; D015398:Signal Transduction / Q000235:genetics / Q000502:physiology*
D009711:Nucleotides; D010750:Phosphoproteins; D000075223:Poly-ADP-Ribose Binding Proteins; D000246:Adenosine Diphosphate Ribose; C520557:APLF protein, human; D043603:DNA-(Apurinic or Apyrimidinic Site) Lyase