8jnr
From Proteopedia
Crystal structure of human ALKBH3 bound to 3mC containing ssDNA through distal crosslink
Structural highlights
FunctionALKB3_HUMAN Dioxygenase that mediates demethylation of DNA and RNA containing 1-methyladenosine (m1A) (PubMed:12486230, PubMed:12594517, PubMed:16174769, PubMed:26863196, PubMed:26863410). Repairs alkylated DNA containing 1-methyladenosine (m1A) and 3-methylcytosine (m3C) by oxidative demethylation (PubMed:12486230, PubMed:12594517, PubMed:16174769, PubMed:25944111). Has a strong preference for single-stranded DNA (PubMed:12486230, PubMed:12594517, PubMed:16174769, PubMed:20714506). Able to process alkylated m3C within double-stranded regions via its interaction with ASCC3, which promotes DNA unwinding to generate single-stranded substrate needed for ALKBH3 (PubMed:22055184). Can repair exocyclic 3,N4-ethenocytosine adducs in single-stranded DNA (PubMed:25797601). Also acts on RNA (PubMed:12594517, PubMed:16174769, PubMed:16858410, PubMed:26863196, PubMed:26863410). Demethylates N(1)-methyladenosine (m1A) RNA, an epigenetic internal modification of messenger RNAs (mRNAs) highly enriched within 5'-untranslated regions (UTRs) and in the vicinity of start codons (PubMed:26863196, PubMed:26863410). Requires molecular oxygen, alpha-ketoglutarate and iron (PubMed:16858410, PubMed:22055184).[1] [2] [3] [4] [5] [6] [7] [8] [9] Publication Abstract from PubMedN(1) -methyladenosine (m(1) 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)/alpha-ketoglutarate-dependent dioxygenase family member ALKBH3 is the only known mRNA m(1) 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 beta-hairpins (beta4-loop-beta5 and beta'-loop-beta) and the alpha2 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(1) A- and 3-methylcytidine (m(3) C)-modified substrates. Mutation of Thr133 to the corresponding residue in the AlkB Fe(II)/alpha-ketoglutarate-dependent dioxygenase family members FTO or ALKBH5 converted ALKBH3 substrate selectivity from m(1) A to N(6) -methyladenosine (m(6) A), as did Asp194 deletion. Our findings provide a molecular basis for understanding the mechanisms of substrate recognition and m(1) A demethylation by ALKBH3. This study is expected to aid structure-guided design of chemical probes for further functional studies and therapeutic applications. The Molecular Basis of Human ALKBH3 Mediated RNA N(1) -methyladenosine (m(1) A) Demethylation.,Zhang L, Duan HC, Paduch M, Hu J, Zhang C, Mu Y, Lin H, He C, Kossiakoff AA, Jia G, Zhang L Angew Chem Int Ed Engl. 2024 Feb 12;63(7):e202313900. doi: , 10.1002/anie.202313900. Epub 2024 Jan 11. PMID:38158383[10] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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