Structural Characterization of a Mouse Ortholog of Human NEIL3 with a Marked Preference for Single-Stranded DNA

• Published in: Structure (London) 2013-02, Vol.21 (2), p.247-256
• Main Authors: Liu, Minmin, Imamura, Kayo, Averill, April M., Wallace, Susan S., Doublié, Sylvie
• Format: Article
• Language: English
• Subjects: Amino Acid Motifs; Animals; Backbone; Bacteria; Catalytic Domain; Crystallography, X-Ray; Deoxyribonucleic acid; DNA, Single-Stranded - chemistry; Electrostatics; Endodeoxyribonucleases - chemistry; Enzymes; Humans; Hydrogen Bonding; Mice; Models, Molecular; Nucleic Acid Conformation; Phosphates; Protein Binding; Protein Stability; Protein Structure, Secondary; Residues; Strands; Substrate Specificity; Surface Properties
• ISSN: 0969-2126; 1878-4186
• DOI: 10.1016/j.str.2012.12.008

Endonuclease VIII-like 3 (Neil3) is a DNA glycosylase of the base excision repair pathway that protects cells from oxidative DNA damage by excising a broad spectrum of cytotoxic and mutagenic base lesions. Interestingly, Neil3 exhibits an unusual preference for DNA with single-stranded regions. Here, we report the 2.0 Å crystal structure of a Neil3 enzyme. Although the glycosylase region of mouse Neil3 (MmuNeil3Δ324) exhibits the same overall fold as that of other Fpg/Nei proteins, it presents distinct structural features. First, MmuNeil3Δ324 lacks the αF-β9/10 loop that caps the flipped-out 8-oxoG in bacterial Fpg, which is consistent with its inability to cleave 8-oxoguanine. Second, Neil3 not only lacks two of the three void-filling residues that stabilize the opposite strand, but it also harbors negatively charged residues that create an unfavorable electrostatic environment for the phosphate backbone of that strand. These structural features provide insight into the substrate specificity and marked preference of Neil3 for ssDNA. [Display omitted] ► Neil3 is an Fpg/Nei DNA glycosylase of the base excision repair pathway ► Neil3 excises a broad spectrum of base lesions, with a marked preference for ssDNA ► We report a crystal structure of Neil3 DNA glycosylase ► The structure provides valuable insights into Neil3′s unusual substrate specificity NA glycosylases are enzymes that scan the DNA and excise oxidatively-induced DNA lesions. Liu et al. present a crystal structure of endonuclease VIII-like 3 (Neil3), a glycosylase with a strong preference for single-stranded DNA. The structure provides valuable insights into Neil3's unusual substrate specificity.