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Nat Struct Mol Biol. 2017 Feb;24(2):131-139. doi: 10.1038/nsmb.3344. Epub 2016 Dec 19.

Structural basis for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B.

Shi K1,2,3, Carpenter MA1,2,3,4,5, Banerjee S6, Shaban NM1,2,3,4, Kurahashi K1,2,3, Salamango DJ1,2,3,4, McCann JL1,2,3,4, Starrett GJ1,2,3,4, Duffy JV1,2,3, Demir Ö7, Amaro RE7, Harki DA2,8, Harris RS1,2,3,4,5, Aihara H1,2,3.

Author information

  • 1Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota, USA.
  • 2Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota, USA.
  • 3Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota, USA.
  • 4Center for Genome Engineering, University of Minnesota, Minneapolis, Minnesota, USA.
  • 5Howard Hughes Medical Institute, University of Minnesota, Minneapolis, Minnesota, USA.
  • 6Northeastern Collaborative Access Team, Cornell University, Advanced Photon Source, Lemont, Illinois, USA.
  • 7Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA.
  • 8Department of Medicinal Chemistry, University of Minnesota, Minneapolis, Minnesota, USA.

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.

PMID:
27991903
PMCID:
PMC5296220
[Available on 2017-06-19]
DOI:
10.1038/nsmb.3344
[PubMed - in process]
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