Crystal structure of the catalytic domain of an adenosine deaminase that acts on RNA (hADAR2) bound to inositol hexakisphosphate (IHP)
Classification:
HYDROLASE
Technique:
X-Ray Diffraction
Resolution:
1.7
R value free:
0.206
R value observed:
0.175
R value work:
0.173
Abstract of the PDB Structure's related Publication:
We report the crystal structure of the catalytic domain of human ADAR2, an RNA editing enzyme, at 1.7 angstrom resolution. The structure reveals a zinc ion in the active site and suggests how the substrate adenosine is recognized. Unexpectedly, inositol hexakisphosphate (IP6) is buried within the enzyme core, contributing to the protein fold. Although there are no reports that adenosine deaminases that act on RNA (ADARs) require a cofactor, we show that IP6 is required for activity. Amino acids that coordinate IP6 in the crystal structure are conserved in some adenosine deaminases that act on transfer RNA (tRNA) (ADATs), related enzymes that edit tRNA. Indeed, IP6 is also essential for in vivo and in vitro deamination of adenosine 37 of tRNAala by ADAT1.
Double-stranded RNA-specific adenosine deaminase enzymes (DSRAD) belong to the Adenosine deaminase acting on RNA (ADAR) gene family. Being an highly conserved group of enzymes they share a conserved domain architecture consisting of a variable number of N-terminal dsRNA binding domains (dsRBDs) and a C-terminal catalytic deaminase domain (Savva et al. 2012 ). ADAR is responsible for three modification along BLCAP mRNA that change the encoded protein, downstream of translation (Savva et al. 2012 ). These modifications bring to 8 possible BLCAP isoforms, with an amino acid switch from Y to C, Q to R, and K to R. ADARB1 modifies 5b and 5c positions in the BLCAP of 3'UTR. The distribution of serotonin (5HT)2C receptor (5HT2CR) in the brain suggests specific roles in normal physiology and in disease development such as in the case of, obesity, anxiety, epilepsy, sleep disorders, and motor dysfunction when dysregulated. 5HT2CR's mRNA secondary structure differences between human, mouse, and rat transcripts suggest that ADAR does not have an intrinsic ability to recognize consensus sequences within its substrates. ADAR and ADARB1 edit AUA, AAU, and AUU codons in 5HT2CR that translate for Isoleucine 156 (I156), Asparagine 158 (N158), and I 160 (I160), along the translated protein. Editing sites in 5HT2CR are A, B, C, C', and D, placed in the first and third, first and second, and first coding positions of the three editing codons, respectively. A, B, C, C', and D are in the 466, 468, 472, 473, and 478 nucleotide positions, respectively. Thirtytwo editing-derived permutations are virtually possible. Nevertheless, only two editing profiles have been experimentally observed, among which is the unedited profile.
In the partially edited profile, A and D sites are edited by ADAR and ADARB1, respectively. In the fully edited profile also B, C, and C' sites are edited by both of the two active ADAR isoforms. It appears that a cross-talk between ADAR isoforms exists and influences the modification profile of the intra-exonic region of the 5HT2CR, determined by the relative expression of ADAR and ADARB1. Therefore, an interplay between the two enzymes on the shared editing sites is tempting to be inferred.
(Werry et al. 2008 ) α3 subunit of the GABAA receptor is an editing substrate for either ADAR and ADARB1. Editing of the third codon position of AUA codon triggers the I:M amino acid change, in the translated protein. Given the increasing editing extent that starts at birth and becomes close to 100% in the adult brain, it has been suggested that editing of Gabra-3 mRNA is important for normal brain development.(
Ohlson et al. 2007)