Structures of human ADAR2 bound to dsRNA reveal base-flipping mechanism and basis for site selectivity

Nat Struct Mol Biol. 2016 May;23(5):426-33. doi: 10.1038/nsmb.3203. Epub 2016 Apr 11.

Abstract

Adenosine deaminases acting on RNA (ADARs) are editing enzymes that convert adenosine to inosine in duplex RNA, a modification reaction with wide-ranging consequences in RNA function. Understanding of the ADAR reaction mechanism, the origin of editing-site selectivity, and the effect of mutations is limited by the lack of high-resolution structural data for complexes of ADARs bound to substrate RNAs. Here we describe four crystal structures of the human ADAR2 deaminase domain bound to RNA duplexes bearing a mimic of the deamination reaction intermediate. These structures, together with structure-guided mutagenesis and RNA-modification experiments, explain the basis of the ADAR deaminase domain's dsRNA specificity, its base-flipping mechanism, and its nearest-neighbor preferences. In addition, we identified an ADAR2-specific RNA-binding loop near the enzyme active site, thus rationalizing differences in selectivity observed between different ADARs. Finally, our results provide a structural framework for understanding the effects of ADAR mutations associated with human disease.

Publication types

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

MeSH terms

  • Adenosine Deaminase / chemistry*
  • Base Sequence
  • Biocatalysis
  • Catalytic Domain
  • Crystallography, X-Ray
  • Humans
  • Hydrogen Bonding
  • Kinetics
  • Models, Molecular
  • Protein Binding
  • RNA, Double-Stranded / chemistry*
  • RNA-Binding Proteins / chemistry*
  • Substrate Specificity

Substances

  • RNA, Double-Stranded
  • RNA-Binding Proteins
  • ADARB1 protein, human
  • Adenosine Deaminase