4OCT

Crystal structure of human ALKBH5 crystallized in the presence of Mn^{2+} and 2-oxoglutarate

Summary for 4OCT

• Entry DOI: 10.2210/pdb4oct/pdb
• Descriptor: RNA demethylase ALKBH5, MANGANESE (II) ION, 2-OXOGLUTARIC ACID, ... (5 entities in total)
• Functional Keywords: structural genomics, structural genomics consortium, sgc, rna demethylase, oxidoreductase
• Biological source: Homo sapiens (human)
• Cellular location: Nucleus speckle : Q6P6C2
• Total number of polymer chains: 2
• Total formula weight: 51080.09

Authors

Tempel, W.,Chao, X.,Liu, K.,Dong, A.,Cerovina, T.,He, H.,Bountra, C.,Arrowsmith, C.H.,Edwards, A.M.,Min, J.,Structural Genomics Consortium (SGC) (deposition date: 2014-01-09, release date: 2014-04-16, Last modification date: 2024-11-20)

Primary citation

Xu, C.,Liu, K.,Tempel, W.,Demetriades, M.,Aik, W.,Schofield, C.J.,Min, J.
Structures of human ALKBH5 demethylase reveal a unique binding mode for specific single-stranded N6-methyladenosine RNA demethylation.
J.Biol.Chem., 289:17299-17311, 2014

PubMed Abstract: N(6)-Methyladenosine (m(6)A) is the most prevalent internal RNA modification in eukaryotes. ALKBH5 belongs to the AlkB family of dioxygenases and has been shown to specifically demethylate m(6)A in single-stranded RNA. Here we report crystal structures of ALKBH5 in the presence of either its cofactors or the ALKBH5 inhibitor citrate. Catalytic assays demonstrate that the ALKBH5 catalytic domain can demethylate both single-stranded RNA and single-stranded DNA. We identify the TCA cycle intermediate citrate as a modest inhibitor of ALKHB5 (IC50, ∼488 μm). The structural analysis reveals that a loop region of ALKBH5 is immobilized by a disulfide bond that apparently excludes the binding of dsDNA to ALKBH5. We identify the m(6)A binding pocket of ALKBH5 and the key residues involved in m(6)A recognition using mutagenesis and ITC binding experiments.

PubMed: 24778178
DOI: 10.1074/jbc.M114.550350

Experimental method

X-RAY DIFFRACTION (2.28 Å)