Solution structure and DNA binding of the zinc-finger domain from DNA ligase IIIalpha.
DNA ligase IIIalpha carries out the final ligation step in the base excision repair (BER) and single strand break repair (SSBR) mechanisms of DNA repair. The enzyme recognises single-strand nicks and other damage features in double-stranded DNA, both through the catalytic domain and an N-terminal domain containing a single zinc finger. The latter is homologous to other zinc fingers that recognise damaged DNA, two in the N terminus of poly(adenosine-ribose)polymerase and three in the N terminus of the Arabidopsis thaliana nick-sensing DNA 3'-phosphoesterase. Here, we present the solution structure of the zinc-finger domain of human DNA ligase IIIalpha, the first structure of a finger from this group. It is related to that of the erythroid transcription factor GATA-1, but has an additional N-terminal beta-strand and C-terminal alpha-helix. Chemical shift mapping using a DNA ligand containing a single-stranded break showed that the DNA-binding surface of the DNA-ligase IIIalpha zinc finger is substantially different from that of GATA-1, consistent with the fact that the two proteins recognise very different features in the DNA. Likely implications for DNA binding are discussed.
MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK.
Arkadiusz W
AW
Kulczyk
Ji-Chun
JC
Yang
David
D
Neuhaus
D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000201:enzymology; D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D000072481:DNA Ligase ATP; D011088:DNA Ligases / Q000737:chemistry*; D004260:DNA Repair; D004268:DNA-Binding Proteins / Q000378:metabolism; D019992:Databases as Topic; D050981:Erythroid-Specific DNA-Binding Factors; D004926:Escherichia coli / Q000378:metabolism; D008024:Ligands; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D000075223:Poly-ADP-Ribose Binding Proteins; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D012984:Software; D014157:Transcription Factors / Q000378:metabolism; D029867:Xenopus Proteins; D016335:Zinc Fingers
D004268:DNA-Binding Proteins; D050981:Erythroid-Specific DNA-Binding Factors; D008024:Ligands; D000075223:Poly-ADP-Ribose Binding Proteins; D014157:Transcription Factors; D029867:Xenopus Proteins; D004247:DNA; D011088:DNA Ligases; D000072481:DNA Ligase ATP; C000618816:DNA ligase III alpha protein, Xenopus