Interaction of JMJD6 with single-stranded RNA

JMJD6 is a Jumonji C domain-containing hydroxylase. JMJD6 binds α-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 α-ketoglutarate, which revealed a novel substrate bindi...

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Bibliographic Details
Published in:Proceedings of the National Academy of Sciences - PNAS 2010-08, Vol.107 (33), p.14568-14572
Main Authors: Hong, Xia, Zang, Jianye, White, Janice, Wang, Chao, Pan, Cheol-Ho, Zhao, Rui, Murphy, Robert C., Dai, Shaodong, Henson, Peter, Kappler, John W., Hagman, James, Zhang, Gongyi
Format: Article
Language:English
Subjects:
Apoptosis
Arginine
Aromatics
Binding sites
Binding Sites - genetics
Binding, Competitive
Biological Sciences
Conformation
Crystals
Deoxyribonucleic acid
DNA
DNA - chemistry
DNA - metabolism
DNA, Single-Stranded - chemistry
DNA, Single-Stranded - metabolism
Double-stranded RNA
Electrophoretic Mobility Shift Assay
Enzymes
Family structure
Histones
Humans
Hydroxylase
Iron
Jumonji Domain-Containing Histone Demethylases - chemistry
Jumonji Domain-Containing Histone Demethylases - genetics
Jumonji Domain-Containing Histone Demethylases - metabolism
Models, Molecular
Molecular structure
Nucleic Acid Conformation
Peptides
Phosphatidylserines
Procollagen-lysine 5-dioxygenase
Protein Binding
Protein Structure, Tertiary
Proteins
Receptors
Ribonucleic acid
RNA
RNA - chemistry
RNA - metabolism
RNA, Double-Stranded - chemistry
RNA, Double-Stranded - metabolism
Substrate Specificity
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Summary:JMJD6 is a Jumonji C domain-containing hydroxylase. JMJD6 binds α-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 α-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.
ISSN:0027-8424
1091-6490
DOI:10.1073/pnas.1008832107