title: Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B.
abstract: APOBEC-catalyzed cytosine-to-uracil deamination of single-stranded DNA (ssDNA) has beneficial functions in immunity and detrimental effects in cancer. APOBEC enzymes have intrinsic dinucleotide specificities that impart hallmark mutation signatures. Although numerous structures have been solved, mechanisms for global ssDNA recognition and local target-sequence selection remain unclear. Here we report crystal structures of human APOBEC3A and a chimera of human APOBEC3B and APOBEC3A bound to ssDNA at 3.1-Å and 1.7-Å resolution, respectively. These structures reveal a U-shaped DNA conformation, with the specificity-conferring -1 thymine flipped out and the target cytosine inserted deep into the zinc-coordinating active site pocket. The -1 thymine base fits into a groove between flexible loops and makes direct hydrogen bonds with the protein, accounting for the strong 5'-TC preference. These findings explain both conserved and unique properties among APOBEC family members, and they provide a basis for the rational design of inhibitors to impede the evolvability of viruses and tumors.
authors.affiliation: Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA.|Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA.|Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA.
authors.forename: Ke
authors.initials: K
authors.lastname: Shi
authors.affiliation: Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA.|Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA.|Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA.|Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA.|Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, USA.
authors.forename: Michael A
authors.initials: MA
authors.lastname: Carpenter
authors.affiliation: Northeastern Collaborative Access Team, Cornell University, Advanced Photon Source, Lemont, Illinois, USA.
authors.forename: Surajit
authors.initials: S
authors.lastname: Banerjee
authors.affiliation: Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA.|Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA.|Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA.|Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA.
authors.forename: Nadine M
authors.initials: NM
authors.lastname: Shaban
authors.affiliation: Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA.|Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA.|Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA.
authors.forename: Kayo
authors.initials: K
authors.lastname: Kurahashi
authors.affiliation: Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA.|Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA.|Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA.|Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Salamango
authors.affiliation: Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA.|Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA.|Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA.|Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA.
authors.forename: Jennifer L
authors.initials: JL
authors.lastname: McCann
authors.affiliation: Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA.|Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA.|Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA.|Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA.
authors.forename: Gabriel J
authors.initials: GJ
authors.lastname: Starrett
authors.affiliation: Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA.|Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA.|Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA.
authors.forename: Justin V
authors.initials: JV
authors.lastname: Duffy
authors.affiliation: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA.
authors.forename: Özlem
authors.initials: Ö
authors.lastname: Demir
authors.affiliation: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA.
authors.forename: Rommie E
authors.initials: RE
authors.lastname: Amaro
authors.affiliation: Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA.|Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, USA.
authors.forename: Daniel A
authors.initials: DA
authors.lastname: Harki
authors.affiliation: Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA.|Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA.|Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA.|Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA.|Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, USA.
authors.forename: Reuben S
authors.initials: RS
authors.lastname: Harris
authors.affiliation: Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA.|Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA.|Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA.
authors.forename: Hideki
authors.initials: H
authors.lastname: Aihara
mesh_terms: D000586:Amination; D001483:Base Sequence; D001665:Binding Sites; D020134:Catalytic Domain; D016384:Consensus Sequence; D018360:Crystallography, X-Ray; D003564:Cytidine Deaminase / Q000737:chemistry* / Q000502:physiology; D003596:Cytosine; D004277:DNA, Single-Stranded / Q000737:chemistry; D006801:Humans; D006860:Hydrogen Bonding; D007700:Kinetics; D015778:Minor Histocompatibility Antigens / Q000737:chemistry* / Q000502:physiology; D008958:Models, Molecular; D016296:Mutagenesis; D011485:Protein Binding; D000072756:Protein Conformation, alpha-Helical; D011506:Proteins / Q000737:chemistry* / Q000502:physiology; D013379:Substrate Specificity
chemical_list: D004277:DNA, Single-Stranded; D015778:Minor Histocompatibility Antigens; D011506:Proteins; D003596:Cytosine; C121399:APOBEC3A protein, human; C495794:APOBEC3B protein, human; D003564:Cytidine Deaminase