title: Crystal Structure of the DNA Deaminase APOBEC3B Catalytic Domain.
abstract: Functional and deep sequencing studies have combined to demonstrate the involvement of APOBEC3B in cancer mutagenesis. APOBEC3B is a single-stranded DNA cytosine deaminase that functions normally as a nuclear-localized restriction factor of DNA-based pathogens. However, it is overexpressed in cancer cells and elicits an intrinsic preference for 5'-TC motifs in single-stranded DNA, which is the most frequently mutated dinucleotide in breast, head/neck, lung, bladder, cervical, and several other tumor types. In many cases, APOBEC3B mutagenesis accounts for the majority of both dispersed and clustered (kataegis) cytosine mutations. Here, we report the first structures of the APOBEC3B catalytic domain in multiple crystal forms. These structures reveal a tightly closed active site conformation and suggest that substrate accessibility is regulated by adjacent flexible loops. Residues important for catalysis are identified by mutation analyses, and the results provide insights into the mechanism of target site selection. We also report a nucleotide (dCMP)-bound crystal structure that informs a multistep model for binding single-stranded DNA. Overall, these high resolution crystal structures provide a framework for further mechanistic studies and the development of novel anti-cancer drugs to inhibit this enzyme, dampen tumor evolution, and minimize adverse outcomes such as drug resistance and metastasis.
authors.affiliation: Department of Biochemistry, Molecular Biology, and Biophysics; Institute for Molecular Virology; Masonic Cancer Center. Electronic address: rsh@umn.edu.
authors.forename: Ke
authors.initials: K
authors.lastname: Shi
authors.affiliation: Department of Biochemistry, Molecular Biology, and Biophysics; Institute for Molecular Virology; Masonic Cancer Center.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Carpenter
authors.affiliation: Department of Biochemistry, Molecular Biology, and Biophysics; Institute for Molecular Virology; Masonic Cancer Center.
authors.forename: Kayo
authors.initials: K
authors.lastname: Kurahashi
authors.affiliation: Department of Biochemistry, Molecular Biology, and Biophysics; Institute for Molecular Virology; Masonic Cancer Center; Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota 55455.
authors.forename: Reuben S
authors.initials: RS
authors.lastname: Harris
authors.affiliation: Department of Biochemistry, Molecular Biology, and Biophysics; Institute for Molecular Virology; Masonic Cancer Center.
authors.forename: Hideki
authors.initials: H
authors.lastname: Aihara
mesh_terms: D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D003564:Cytidine Deaminase / Q000737:chemistry*; D004795:Enzyme Stability; D006801:Humans; D015778:Minor Histocompatibility Antigens; D008958:Models, Molecular; D011487:Protein Conformation; D012995:Solubility
chemical_list: D015778:Minor Histocompatibility Antigens; C495794:APOBEC3B protein, human; D003564:Cytidine Deaminase
keywords: APOBEC3B; DNA binding protein; DNA deaminase; DNA editing; DNA repair; Mutation; cancer; cancer mutagenesis; crystal structure; enzyme mutation