title: Interaction of JMJD6 with single-stranded RNA.
abstract: JMJD6 is a Jumonji C domain-containing hydroxylase. JMJD6 binds alpha-ketoglutarate and iron and has been characterized as either a histone arginine demethylase or U2AF65 lysyl hydroxylase. Here, we describe the structures of JMJD6 with and without alpha-ketoglutarate, which revealed a novel substrate binding groove and two positively charged surfaces. The structures also contain a stack of aromatic residues located near the active center. The side chain of one residue within this stack assumed different conformations in the two structures. Interestingly, JMJD6 bound efficiently to single-stranded RNA, but not to single-stranded DNA, double-stranded RNA, or double-stranded DNA. These structural features and truncation analysis of JMJD6 suggest that JMJD6 may bind and modify single-stand RNA rather than the previously reported peptide substrates.
authors.affiliation: Integrated Department of Immunology, National Jewish Health, Denver, CO 80206.
authors.forename: Xia
authors.initials: X
authors.lastname: Hong
authors.forename: Jianye
authors.initials: J
authors.lastname: Zang
authors.forename: Janice
authors.initials: J
authors.lastname: White
authors.forename: Chao
authors.initials: C
authors.lastname: Wang
authors.forename: Cheol-Ho
authors.initials: CH
authors.lastname: Pan
authors.forename: Rui
authors.initials: R
authors.lastname: Zhao
authors.forename: Robert C
authors.initials: RC
authors.lastname: Murphy
authors.forename: Shaodong
authors.initials: S
authors.lastname: Dai
authors.forename: Peter
authors.initials: P
authors.lastname: Henson
authors.forename: John W
authors.initials: JW
authors.lastname: Kappler
authors.forename: James
authors.initials: J
authors.lastname: Hagman
authors.forename: Gongyi
authors.initials: G
authors.lastname: Zhang
mesh_terms: D001665:Binding Sites / Q000235:genetics; D001667:Binding, Competitive; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004277:DNA, Single-Stranded / Q000737:chemistry / Q000378:metabolism; D024202:Electrophoretic Mobility Shift Assay; D006801:Humans; D056484:Jumonji Domain-Containing Histone Demethylases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D012313:RNA / Q000737:chemistry* / Q000378:metabolism; D012330:RNA, Double-Stranded / Q000737:chemistry / Q000378:metabolism; D013379:Substrate Specificity
chemical_list: D004277:DNA, Single-Stranded; D012330:RNA, Double-Stranded; D012313:RNA; D004247:DNA; D056484:Jumonji Domain-Containing Histone Demethylases; C524220:KDM6B protein, human