9D5K

Human Adenosine Deaminase Acting on dsRNA (ADAR2-RD) bound to dsRNA containing an expanded cytidine analog at the -1 position of the guide strand

This is a non-PDB format compatible entry.

Summary for 9D5K

• Entry DOI: 10.2210/pdb9d5k/pdb
• Related: 6VFF 8E0F 8E4X
• Descriptor: Isoform 4 of Double-stranded RNA-specific editase 1, RNA Top Strand, RNA Bottom Strand, ... (7 entities in total)
• Functional Keywords: adenosine deaminase, dsrna, complex, rna editing, cytidine analog, rna binding protein, rna binding protein-rna complex, rna binding protein/rna
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 4
• Total formula weight: 129932.92

Authors

Fisher, A.J.,Cheng, J.,Manjunath, A.,Campbell, K. (deposition date: 2024-08-13, release date: 2024-11-06)

Primary citation

Manjunath, A.,Cheng, J.,Campbell, K.B.,Jacobsen, C.S.,Mendoza, H.G.,Bierbaum, L.,Jauregui-Matos, V.,Doherty, E.E.,Fisher, A.J.,Beal, P.A.
Nucleoside Analogs in ADAR Guide Strands Enable Editing at 5'-G A Sites.
Biomolecules, 14:-, 2024

PubMed Abstract: Adenosine Deaminases Acting on RNA (ADARs) are members of a family of RNA editing enzymes that catalyze the conversion of adenosine into inosine in double-stranded RNA (dsRNA). ADARs' selective activity on dsRNA presents the ability to correct mutations at the transcriptome level using guiding oligonucleotides. However, this approach is limited by ADARs' preference for specific sequence contexts to achieve efficient editing. Substrates with a guanosine adjacent to the target adenosine in the 5' direction (5'-GA) are edited less efficiently compared to substrates with any other canonical nucleotides at this position. Previous studies showed that a G/purine mismatch at this position results in more efficient editing than a canonical G/C pair. Herein, we investigate a series of modified oligonucleotides containing purine or size-expanded nucleoside analogs on guide strands opposite the 5'-G (-1 position). The results demonstrate that modified adenosine and inosine analogs enhance editing at 5'-GA sites. Additionally, the inclusion of a size-expanded cytidine analog at this position improves editing over a control guide bearing cytidine. High-resolution crystal structures of ADAR:/RNA substrate complexes reveal the manner by which both inosine and size-expanded cytidine are capable of activating editing at 5'-GA sites. Further modification of these altered guide sequences for metabolic stability in human cells demonstrates that the incorporation of specific purine analogs at the -1 position significantly improves editing at 5'-GA sites.

PubMed: 39456162
DOI: 10.3390/biom14101229

Experimental method

X-RAY DIFFRACTION (2.697 Å)