8JNK

Crystal structure of human ALKBH3 bound to ssDNA through active site crosslink

Summary for 8JNK

• Entry DOI: 10.2210/pdb8jnk/pdb
• Descriptor: Alpha-ketoglutarate-dependent dioxygenase alkB homolog 3, DNA, Synthetic antibody heavy chain, ... (7 entities in total)
• Functional Keywords: rna m1a demethylase, rna binding protein
• Biological source: Homo sapiens (human); More
• Total number of polymer chains: 16
• Total formula weight: 302617.94

Authors

Zhang, L. (deposition date: 2023-06-06, release date: 2024-01-24, Last modification date: 2024-11-13)

Primary citation

Zhang, L.,Duan, H.C.,Paduch, M.,Hu, J.,Zhang, C.,Mu, Y.,Lin, H.,He, C.,Kossiakoff, A.A.,Jia, G.,Zhang, L.
The Molecular Basis of Human ALKBH3 Mediated RNA N 1 -methyladenosine (m 1 A) Demethylation.
Angew.Chem.Int.Ed.Engl., 63:e202313900-e202313900, 2024

PubMed Abstract: N -methyladenosine (m A) is a prevalent post-transcriptional RNA modification, and the distribution and dynamics of the modification play key epitranscriptomic roles in cell development. At present, the human AlkB Fe(II)/α-ketoglutarate-dependent dioxygenase family member ALKBH3 is the only known mRNA m A demethylase, but its catalytic mechanism remains unclear. Here, we present the structures of ALKBH3-oligo crosslinked complexes obtained with the assistance of a synthetic antibody crystallization chaperone. Structural and biochemical results showed that ALKBH3 utilized two β-hairpins (β4-loop-β5 and β'-loop-β'') and the α2 helix to facilitate single-stranded substrate binding. Moreover, a bubble-like region around Asp194 and a key residue inside the active pocket (Thr133) enabled specific recognition and demethylation of m A- and 3-methylcytidine (m C)-modified substrates. Mutation of Thr133 to the corresponding residue in the AlkB Fe(II)/α-ketoglutarate-dependent dioxygenase family members FTO or ALKBH5 converted ALKBH3 substrate selectivity from m A to N -methyladenosine (m A), as did Asp194 deletion. Our findings provide a molecular basis for understanding the mechanisms of substrate recognition and m A demethylation by ALKBH3. This study is expected to aid structure-guided design of chemical probes for further functional studies and therapeutic applications.

PubMed: 38158383
DOI: 10.1002/anie.202313900

Experimental method

X-RAY DIFFRACTION (2.69 Å)