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Yue W.W.,University of Oxford | Hozjan V.,University of Oxford | Ge W.,University of Oxford | Loenarz C.,University of Oxford | And 6 more authors.
FEBS Letters

Crystallographic analysis of the catalytic domain of PHD finger protein 8 (PHF8), an Nε-methyl lysine histone demethylase associated with mental retardation and cleft lip/palate, reveals a double-stranded β-helix fold with conserved Fe(II) and cosubstrate binding sites typical of the 2-oxoglutarate dependent oxygenases. The PHF8 active site is highly conserved with those of the FBXL10/11demethylases, which are also selective for the di-/mono-methylated lysine states, but differs from that of the JMJD2 demethylases which are selective for tri-/di-methylated states. The results rationalize the lack of activity for the clinically observed F279S PHF8 variant and they will help to identify inhibitors selective for specific Nε-methyl lysine demethylase subfamilies. © 2010. Source

Zhang Z.,University of Oxford | Kochan G.T.,Old Road Campus Research Building | Kochan G.T.,The Botnar Research Center | Ng S.S.,Old Road Campus Research Building | And 7 more authors.
Biochemical and Biophysical Research Communications

Phytanoyl-CoA hydroxylase (PAHX) catalyzes an important step in the metabolism of the fatty acid side chain of chlorophyll. PHYHD1 exists in three isoforms and is the closest human homologue of PAHX. We show that like PAHX, the PHYHD1A but likely not the PHYHD1B/C isoforms, is a functional Fe(II) and 2-oxoglutarate (2OG) dependent oxygenase. Crystallographic and biochemical analyses reveal that PHYHD1A has the double-stranded β-helix fold and Fe(II) and cosubstrate binding residues characteristic of the 2-oxoglutarate dependent oxygenases and catalyzes the conversion of 2-oxoglutarate to succinate and CO2 in an iron-dependent manner. However, PHYHD1A did not couple 2OG turnover to the hydroxylation of acyl-coenzyme A derivatives that are substrates for PAHX, implying that it is not directly involved in phytanoyl coenzyme-A metabolism. © 2011. Source

Rose N.R.,University of Oxford | Woon E.C.Y.,University of Oxford | Kingham G.L.,University of Oxford | King O.N.F.,University of Oxford | And 9 more authors.
Journal of Medicinal Chemistry

Ferrous ion and 2-oxoglutarate (2OG) oxygenases catalyze the demethylation of Ne-methylated lysine residues in histones. Here we report studies on the inhibition of the JMJD2 subfamily of histone demethylases, employing binding analyses by nondenaturing mass spectrometry (MS), dynamic combinatorial chemistry coupled to MS, turnover assays, and crystallography. The results of initial binding and inhibition assays directed the production and analysis of a set of N-oxalyl-D-tyrosine derivatives to explore the extent of a subpocket at the JMJD2 active site. Some of the inhibitors were shown to be selective for JMJD2 over the hypoxia-inducible factor prolyl hydroxylase PHD2. A crystal structure of JMJD2A in, complex with one of the potent inhibitors was obtained; modeling other inhibitors based, on this structure predicts interactions that enable improved inhibition for some compounds. © 2010 American Chemical Society. Source

Mantri M.,University of Oxford | Krojer T.,University of Oxford | Krojer T.,The Botnar Research Center | Bagg E.A.,University of Oxford | And 10 more authors.
Journal of Molecular Biology

Lysyl and prolyl hydroxylations are well-known post-translational modifications to animal and plant proteins with extracellular roles. More recent work has indicated that the hydroxylation of intracellular animal proteins may be common. JMJD6 catalyses the iron- and 2-oxoglutarate-dependent hydroxylation of lysyl residues in arginine-serine-rich domains of RNA-splicing-related proteins. We report crystallographic studies on the catalytic domain of JMJD6 in complex with Ni(II) substituting for Fe(II). Together with mutational studies, the structural data suggest how JMJD6 binds its lysyl residues such that it can catalyse C-5 hydroxylation rather than Nε-demethylation, as for analogous enzymes. © 2010 Elsevier Ltd. Source

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