Crystal structure of APOBEC3A bound to single-stranded DNA reveals structural basis for cytidine deamination and specificity

Nat Commun. 2017 Apr 28;8:15024. doi: 10.1038/ncomms15024.

Abstract

Nucleic acid editing enzymes are essential components of the immune system that lethally mutate viral pathogens and somatically mutate immunoglobulins, and contribute to the diversification and lethality of cancers. Among these enzymes are the seven human APOBEC3 deoxycytidine deaminases, each with unique target sequence specificity and subcellular localization. While the enzymology and biological consequences have been extensively studied, the mechanism by which APOBEC3s recognize and edit DNA remains elusive. Here we present the crystal structure of a complex of a cytidine deaminase with ssDNA bound in the active site at 2.2 Å. This structure not only visualizes the active site poised for catalysis of APOBEC3A, but pinpoints the residues that confer specificity towards CC/TC motifs. The APOBEC3A-ssDNA complex defines the 5'-3' directionality and subtle conformational changes that clench the ssDNA within the binding groove, revealing the architecture and mechanism of ssDNA recognition that is likely conserved among all polynucleotide deaminases, thereby opening the door for the design of mechanistic-based therapeutics.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Catalytic Domain*
  • Crystallography, X-Ray
  • Cytidine / chemistry*
  • Cytidine / metabolism
  • Cytidine Deaminase / chemistry*
  • Cytidine Deaminase / genetics
  • Cytidine Deaminase / metabolism
  • DNA, Single-Stranded / chemistry*
  • DNA, Single-Stranded / genetics
  • DNA, Single-Stranded / metabolism
  • Deamination
  • Humans
  • Models, Molecular
  • Protein Binding
  • Protein Domains
  • Protein Structure, Secondary
  • Proteins / chemistry*
  • Proteins / genetics
  • Proteins / metabolism
  • Sequence Homology, Amino Acid
  • Substrate Specificity

Substances

  • DNA, Single-Stranded
  • Proteins
  • Cytidine
  • APOBEC3A protein, human
  • Cytidine Deaminase