title: Crystal structures of histone demethylase JMJD2A reveal basis for substrate specificity.
abstract: Post-translational histone modification has a fundamental role in chromatin biology and is proposed to constitute a 'histone code' in epigenetic regulation. Differential methylation of histone H3 and H4 lysyl residues regulates processes including heterochromatin formation, X-chromosome inactivation, genome imprinting, DNA repair and transcriptional regulation. The discovery of lysyl demethylases using flavin (amine oxidases) or Fe(II) and 2-oxoglutarate as cofactors (2OG oxygenases) has changed the view of methylation as a stable epigenetic marker. However, little is known about how the demethylases are selective for particular lysyl-containing sequences in specific methylation states, a key to understanding their functions. Here we reveal how human JMJD2A (jumonji domain containing 2A), which is selective towards tri- and dimethylated histone H3 lysyl residues 9 and 36 (H3K9me3/me2 and H3K36me3/me2), discriminates between methylation states and achieves sequence selectivity for H3K9. We report structures of JMJD2A-Ni(II)-Zn(II) inhibitor complexes bound to tri-, di- and monomethyl forms of H3K9 and the trimethyl form of H3K36. The structures reveal a lysyl-binding pocket in which substrates are bound in distinct bent conformations involving the Zn-binding site. We propose a mechanism for achieving methylation state selectivity involving the orientation of the substrate methyl groups towards a ferryl intermediate. The results suggest distinct recognition mechanisms in different demethylase subfamilies and provide a starting point to develop chemical tools for drug discovery and to study and dissect the complexity of reversible histone methylation and its role in chromatin biology.
authors.affiliation: Structural Genomics Consortium, Botnar Research Center, University of Oxford, Oxford OX3 7LD, UK.
authors.forename: Stanley S
authors.initials: SS
authors.lastname: Ng
authors.forename: Kathryn L
authors.initials: KL
authors.lastname: Kavanagh
authors.forename: Michael A
authors.initials: MA
authors.lastname: McDonough
authors.forename: Danica
authors.initials: D
authors.lastname: Butler
authors.forename: Ewa S
authors.initials: ES
authors.lastname: Pilka
authors.forename: Benoit M R
authors.initials: BM
authors.lastname: Lienard
authors.forename: James E
authors.initials: JE
authors.lastname: Bray
authors.forename: Pavel
authors.initials: P
authors.lastname: Savitsky
authors.forename: Opher
authors.initials: O
authors.lastname: Gileadi
authors.forename: Frank
authors.initials: F
authors.lastname: von Delft
authors.forename: Nathan R
authors.initials: NR
authors.lastname: Rose
authors.forename: John
authors.initials: J
authors.lastname: Offer
authors.forename: Johanna C
authors.initials: JC
authors.lastname: Scheinost
authors.forename: Tomasz
authors.initials: T
authors.lastname: Borowski
authors.forename: Michael
authors.initials: M
authors.lastname: Sundstrom
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Schofield
authors.forename: Udo
authors.initials: U
authors.lastname: Oppermann
mesh_terms: D001665:Binding Sites; D018360:Crystallography, X-Ray; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000378:metabolism; D006657:Histones / Q000378:metabolism*; D056484:Jumonji Domain-Containing Histone Demethylases; D008958:Models, Molecular; D010089:Oxidoreductases, N-Demethylating / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D011994:Recombinant Proteins; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D013329:Structure-Activity Relationship; D013379:Substrate Specificity; D014157:Transcription Factors / Q000737:chemistry* / Q000378:metabolism
chemical_list: D004268:DNA-Binding Proteins; D006657:Histones; D011994:Recombinant Proteins; D014157:Transcription Factors; D056484:Jumonji Domain-Containing Histone Demethylases; C494424:KDM4A protein, human; D010089:Oxidoreductases, N-Demethylating