Summary information and primary citation
- PDB-id
-
7wkv;
DSSR-derived features in text and
JSON formats; DNAproDB
- Class
- oxidoreductase-RNA
- Method
- X-ray (2.1 Å)
- Summary
- Crystal structure of human alkbh5 in complex with
2-oxoglutarate (2og) and m6a-containing ssrna
- Reference
-
Kaur S, Tam NY, McDonough MA, Schofield CJ, Aik WS
(2022): "Mechanisms
of substrate recognition and N6-methyladenosine
demethylation revealed by crystal structures of
ALKBH5-RNA complexes." Nucleic Acids Res.,
50, 4148-4160. doi: 10.1093/nar/gkac195.
- Abstract
- AlkB homologue 5 (ALKBH5) is a ferrous iron and
2-oxoglutarate dependent oxygenase that demethylates RNA
N6-methyladenosine (m6A), a post-transcriptional RNA
modification with an emerging set of regulatory roles.
Along with the fat mass and obesity-associated protein
(FTO), ALKBH5 is one of only two identified human m6A RNA
oxidizing enzymes and is a potential target for cancer
treatment. Unlike FTO, ALKBH5 efficiently catalyzes
fragmentation of its proposed nascent hemiaminal
intermediate to give formaldehyde and a demethylated
nucleoside. A detailed analysis of the molecular mechanisms
used by ALKBH5 for substrate recognition and m6A
demethylation is lacking. We report three crystal
structures of ALKBH5 in complex with an m6A-ssRNA 8-mer
substrate and supporting biochemical analyses. Strikingly,
the single-stranded RNA substrate binds to the active site
of ALKBH5 in a 5'-3' orientation that is opposite to
single-stranded or double-stranded DNA substrates observed
for other AlkB subfamily members, including single-stranded
DNA bound to FTO. The combined structural and biochemical
results provide insight into the preference of ALKBH5 for
substrates containing a (A/G)m6AC consensus sequence motif.
The results support a mechanism
involving formation of an m6A hemiaminal intermediate,
followed by efficient ALKBH5 catalyzed
demethylation, enabled by a proton shuttle network
involving Lys132 and Tyr139.
