ADAR proteins: double-stranded RNA and Z-DNA binding domains

Abstract

Adenosine deaminases acting on RNA (ADAR) catalyze adenosine to inosine editing within double-stranded RNA (dsRNA) substrates. Inosine is read as a guanine by most cellular processes and therefore these changes create codons for a different amino acid, stop codons or even a new splice-site allowing protein diversity generated from a single gene. We review here the current structural and molecular knowledge on RNA editing by the ADAR family of protein. We focus especially on two types of nucleic acid binding domains present in ADARs, namely the dsRNA and Z-DNA binding domains.

Fig. 1

Deamination of adenosine to inosine by ADAR. a) Hydrolytic deamination converts adenosine to inosine. b) Inosine base-pairs with cytidine and is thus read as a guanine by most cellular processes.

Fig. 2

Domain organization of the ADAR family members. a) The ADAR family members are represented with their domain structure organization. Three ADARs are found in vertebrates (ADAR1—3). One ADAR is found in D. melanogaster (dADAR) and two in C. elegans (CeADAR1—2). ADARs have a conserved C-terminal deaminase domain (in yellow) and diverse numbers of dsRNA binding domains (in blue). In addition ADAR1 has one or two copies of Z-DNA binding domains (in green). The long isoform of ADAR1 is interferon-inducible (ADAR1-i) whereas the short isoform is constitutively expressed (ADAR1-c). ADAR3 has an arginine-rich R domain (in red). b) Sequence alignment of dsRBDs from the ADAR family members. The alignment is colored by amino acid conservation and properties. hADAR2 dsRBD1 secondary structure elements are shown on top of the alignment.

Fig. 3

Structures of various ADAR editing substrates. a) Secondary structure of ADAR editing substrates: GluR-B R/G and Q/R sites, Drosophila sytI I/V site and pri-miR-376a1. b) Structure of the GluR-B GCUAA apical pentaloop (PDB code 1YSV). c) Structure of the RNA helix surrounding the GluR-B R/G site revealing two particular A+•C wobble base-pairs (PDB code 2L2J). d) Hydrogen bond pattern in an A+•C wobble base-pair and comparison with a G•U wobble base-pair.

Fig. 4

Structures of ADAR Z-DNA binding domains. a) Structure of the Zα domain of ADAR1 in complex with Z-DNA (CG)₃ showing contacts with the phosphate backbone via helix α1 and beta hairpin β2-β3. b) Structure of the Zβ domain of ADAR1 in its free state with a nonfunctional Z-DNA binding surface and a potential protein/protein interaction surface. The additional helix α4 is shown in red. c) Sequence alignment of hADAR1 Zα and Zβ domains. The alignment is colored by amino acid conservation and properties. Common secondary structure elements are shown on top of the alignment. The position of the additional helix α4 is shown below. Residues of Zα involved in direct or water-mediated contacts with Z-DNA are reported with black arrows. Some of these residues are not conserved in Zβ. Residue numbers correspond to the one of Zα.

Fig. 5

RNA recognition by ADAR2 dsRBDs through sequence specific readout of the minor groove. a) Structure of ADAR2 dsRBD1 in complex with the GluR-B R/G upper stem-loop (PDB code 2L3C). Overall structure (top) and close-up view of the minor groove sequence-specific recognitions mediated by helix α1 and the β1-β2 loop (bottom). b) Structure of ADAR2 dsRBD2 in complex with the GluR-B R/G lower stem-loop (PDB code 2L2K). Overall structure (top) and close-up view of the minor groove sequence-specific recognitions mediated by helix α1 and the β1-β2 loop (bottom). c) Chemical groups of an A-U pair lying in the major and minor grooves. d) Chemical groups of a G-C pair lying in the major and minor grooves. Discrimination in the minor groove relies on the appreciation of the group in position 2 of purine rings.

Fig. 6

Spatial organization of the two dsRBDs of ADAR2 on the GluR-B R/G site. a) Side view of the complex (PDB code 2L3J). b) Top view of the complex showing the portion of the space covered by the two dsRBDs around the RNA helix. c) Schematic representation of the sequence specific contacts defining the binding register of ADAR2 dsRBD1. d) Schematic representation of the sequence specific contacts defining the binding register of ADAR2 dsRBD2.