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  • 1
    Publication Date: 2019
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 2
    Publication Date: 2001-04-09
    Description: Hypoxia-inducible factor (HIF) is a transcriptional complex that plays a central role in the regulation of gene expression by oxygen. In oxygenated and iron replete cells, HIF-alpha subunits are rapidly destroyed by a mechanism that involves ubiquitylation by the von Hippel-Lindau tumor suppressor (pVHL) E3 ligase complex. This process is suppressed by hypoxia and iron chelation, allowing transcriptional activation. Here we show that the interaction between human pVHL and a specific domain of the HIF-1alpha subunit is regulated through hydroxylation of a proline residue (HIF-1alpha P564) by an enzyme we have termed HIF-alpha prolyl-hydroxylase (HIF-PH). An absolute requirement for dioxygen as a cosubstrate and iron as cofactor suggests that HIF-PH functions directly as a cellular oxygen sensor.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Jaakkola, P -- Mole, D R -- Tian, Y M -- Wilson, M I -- Gielbert, J -- Gaskell, S J -- von Kriegsheim, A -- Hebestreit, H F -- Mukherji, M -- Schofield, C J -- Maxwell, P H -- Pugh, C W -- Ratcliffe, P J -- New York, N.Y. -- Science. 2001 Apr 20;292(5516):468-72. Epub 2001 Apr 5.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Henry Wellcome Building of Genomic Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/11292861" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Ascorbic Acid/pharmacology ; Cell Hypoxia ; DNA-Binding Proteins/chemistry/*metabolism ; Deferoxamine/pharmacology ; Ferrous Compounds/pharmacology ; Humans ; Hydroxylation ; Hydroxyproline/*metabolism ; Hypoxia-Inducible Factor 1 ; Hypoxia-Inducible Factor 1, alpha Subunit ; *Ligases ; Molecular Sequence Data ; Nuclear Proteins/chemistry/*metabolism ; Oxygen/*physiology ; Point Mutation ; Procollagen-Proline Dioxygenase/antagonists & inhibitors/*metabolism ; Protein Structure, Tertiary ; Proteins/*metabolism ; Recombinant Fusion Proteins/metabolism ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; Transcription Factors/chemistry/*metabolism ; Tumor Cells, Cultured ; *Tumor Suppressor Proteins ; *Ubiquitin-Protein Ligases ; Ubiquitins/metabolism ; Von Hippel-Lindau Tumor Suppressor Protein
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2012-07-31
    Description: The jumonji (JMJ) family of histone demethylases are Fe2+- and alpha-ketoglutarate-dependent oxygenases that are essential components of regulatory transcriptional chromatin complexes. These enzymes demethylate lysine residues in histones in a methylation-state and sequence-specific context. Considerable effort has been devoted to gaining a mechanistic understanding of the roles of histone lysine demethylases in eukaryotic transcription, genome integrity and epigenetic inheritance, as well as in development, physiology and disease. However, because of the absence of any selective inhibitors, the relevance of the demethylase activity of JMJ enzymes in regulating cellular responses remains poorly understood. Here we present a structure-guided small-molecule and chemoproteomics approach to elucidating the functional role of the H3K27me3-specific demethylase subfamily (KDM6 subfamily members JMJD3 and UTX). The liganded structures of human and mouse JMJD3 provide novel insight into the specificity determinants for cofactor, substrate and inhibitor recognition by the KDM6 subfamily of demethylases. We exploited these structural features to generate the first small-molecule catalytic site inhibitor that is selective for the H3K27me3-specific JMJ subfamily. We demonstrate that this inhibitor binds in a novel manner and reduces lipopolysaccharide-induced proinflammatory cytokine production by human primary macrophages, a process that depends on both JMJD3 and UTX. Our results resolve the ambiguity associated with the catalytic function of H3K27-specific JMJs in regulating disease-relevant inflammatory responses and provide encouragement for designing small-molecule inhibitors to allow selective pharmacological intervention across the JMJ family.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691848/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4691848/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kruidenier, Laurens -- Chung, Chun-wa -- Cheng, Zhongjun -- Liddle, John -- Che, KaHing -- Joberty, Gerard -- Bantscheff, Marcus -- Bountra, Chas -- Bridges, Angela -- Diallo, Hawa -- Eberhard, Dirk -- Hutchinson, Sue -- Jones, Emma -- Katso, Roy -- Leveridge, Melanie -- Mander, Palwinder K -- Mosley, Julie -- Ramirez-Molina, Cesar -- Rowland, Paul -- Schofield, Christopher J -- Sheppard, Robert J -- Smith, Julia E -- Swales, Catherine -- Tanner, Robert -- Thomas, Pamela -- Tumber, Anthony -- Drewes, Gerard -- Oppermann, Udo -- Patel, Dinshaw J -- Lee, Kevin -- Wilson, David M -- 092809/Wellcome Trust/United Kingdom -- 18358/Arthritis Research UK/United Kingdom -- P30 CA008748/CA/NCI NIH HHS/ -- Canadian Institutes of Health Research/Canada -- Wellcome Trust/United Kingdom -- England -- Nature. 2012 Aug 16;488(7411):404-8. doi: 10.1038/nature11262.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Epinova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline R&D, Medicines Research Centre, Stevenage SG1 2NY, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22842901" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Biocatalysis/drug effects ; Catalytic Domain ; Cells, Cultured ; Enzyme Inhibitors/metabolism/*pharmacology ; Evolution, Molecular ; Histones/chemistry/metabolism ; Humans ; Inhibitory Concentration 50 ; Jumonji Domain-Containing Histone Demethylases/*antagonists & ; inhibitors/chemistry/classification/metabolism ; Lysine/metabolism ; Macrophages/*drug effects/enzymology/*immunology/metabolism ; Methylation/drug effects ; Mice ; Models, Molecular ; Substrate Specificity ; Tumor Necrosis Factor-alpha/biosynthesis
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2014-10-04
    Description: 〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kruidenier, Laurens -- Chung, Chun-wa -- Cheng, Zhongjun -- Liddle, John -- Che, KaHing -- Joberty, Gerard -- Bantscheff, Marcus -- Bountra, Chas -- Bridges, Angela -- Diallo, Hawa -- Eberhard, Dirk -- Hutchinson, Sue -- Jones, Emma -- Katso, Roy -- Leveridge, Melanie -- Mander, Palwinder K -- Mosley, Julie -- Ramirez-Molina, Cesar -- Rowland, Paul -- Schofield, Christopher J -- Sheppard, Robert J -- Smith, Julia E -- Swales, Catherine -- Tanner, Robert -- Thomas, Pamela -- Tumber, Anthony -- Drewes, Gerard -- Oppermann, Udo -- Patel, Dinshaw J -- Lee, Kevin -- Wilson, David M -- 092809/Wellcome Trust/United Kingdom -- England -- Nature. 2014 Oct 2;514(7520):E2. doi: 10.1038/nature13689.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Epinova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline R&D, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK. ; Platform Technology and Science, GlaxoSmithKline R&D, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK. ; Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10065, USA. ; 1] Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK [2] Botnar Research Centre, NIHR Biomedical Research Unit, University of Oxford OX3 7LD, UK. ; Cellzome AG, Meyerhofstrasse 1, 69117 Heidelberg, Germany. ; Structural Genomics Consortium, University of Oxford, Old Road Campus, Roosevelt Drive, Headington OX3 7DQ, UK. ; Botnar Research Centre, NIHR Biomedical Research Unit, University of Oxford OX3 7LD, UK. ; 1] Epinova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline R&D, Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK [2] Pfizer, Biotherapeutics R&D, 200 Cambridgepark Drive, Cambridge, Massachusetts 02140, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25279927" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Enzyme Inhibitors/*pharmacology ; Humans ; Jumonji Domain-Containing Histone Demethylases/*antagonists & inhibitors ; Macrophages/*drug effects/*immunology
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 5
    Publication Date: 2014-05-13
    Description: 2-Oxoglutarate (2OG)-dependent oxygenases have important roles in the regulation of gene expression via demethylation of N-methylated chromatin components and in the hydroxylation of transcription factors and splicing factor proteins. Recently, 2OG-dependent oxygenases that catalyse hydroxylation of transfer RNA and ribosomal proteins have been shown to be important in translation relating to cellular growth, TH17-cell differentiation and translational accuracy. The finding that ribosomal oxygenases (ROXs) occur in organisms ranging from prokaryotes to humans raises questions as to their structural and evolutionary relationships. In Escherichia coli, YcfD catalyses arginine hydroxylation in the ribosomal protein L16; in humans, MYC-induced nuclear antigen (MINA53; also known as MINA) and nucleolar protein 66 (NO66) catalyse histidine hydroxylation in the ribosomal proteins RPL27A and RPL8, respectively. The functional assignments of ROXs open therapeutic possibilities via either ROX inhibition or targeting of differentially modified ribosomes. Despite differences in the residue and protein selectivities of prokaryotic and eukaryotic ROXs, comparison of the crystal structures of E. coli YcfD and Rhodothermus marinus YcfD with those of human MINA53 and NO66 reveals highly conserved folds and novel dimerization modes defining a new structural subfamily of 2OG-dependent oxygenases. ROX structures with and without their substrates support their functional assignments as hydroxylases but not demethylases, and reveal how the subfamily has evolved to catalyse the hydroxylation of different residue side chains of ribosomal proteins. Comparison of ROX crystal structures with those of other JmjC-domain-containing hydroxylases, including the hypoxia-inducible factor asparaginyl hydroxylase FIH and histone N(epsilon)-methyl lysine demethylases, identifies branch points in 2OG-dependent oxygenase evolution and distinguishes between JmjC-containing hydroxylases and demethylases catalysing modifications of translational and transcriptional machinery. The structures reveal that new protein hydroxylation activities can evolve by changing the coordination position from which the iron-bound substrate-oxidizing species reacts. This coordination flexibility has probably contributed to the evolution of the wide range of reactions catalysed by oxygenases.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4066111/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4066111/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Chowdhury, Rasheduzzaman -- Sekirnik, Rok -- Brissett, Nigel C -- Krojer, Tobias -- Ho, Chia-Hua -- Ng, Stanley S -- Clifton, Ian J -- Ge, Wei -- Kershaw, Nadia J -- Fox, Gavin C -- Muniz, Joao R C -- Vollmar, Melanie -- Phillips, Claire -- Pilka, Ewa S -- Kavanagh, Kathryn L -- von Delft, Frank -- Oppermann, Udo -- McDonough, Michael A -- Doherty, Aidan J -- Schofield, Christopher J -- 092809/Wellcome Trust/United Kingdom -- 6947/Cancer Research UK/United Kingdom -- BB/C518230/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/L009846/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- Arthritis Research UK/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Cancer Research UK/United Kingdom -- Medical Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- England -- Nature. 2014 Jun 19;510(7505):422-6. doi: 10.1038/nature13263. Epub 2014 May 11.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Department of Chemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK. ; 1] The Department of Chemistry and Oxford Centre for Integrative Systems Biology, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK [2]. ; 1] Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK [2]. ; Structural Genomics Consortium, University of Oxford, Headington, Oxford OX3 7DQ, UK. ; Synchrotron SOLEIL, Saint Aubin, 91192 Gif-sur-Yvette Cedex, France. ; 1] Structural Genomics Consortium, University of Oxford, Headington, Oxford OX3 7DQ, UK [2] NIHR Oxford Biomedical Research Unit, Botnar Research Centre, Oxford OX3 7LD, UK. ; Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/24814345" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Catalytic Domain ; Conserved Sequence ; Eukaryota/classification/*enzymology ; Humans ; *Models, Molecular ; Oxygenases/*chemistry/metabolism ; Phylogeny ; Prokaryotic Cells/classification/*enzymology ; Protein Folding ; Protein Structure, Tertiary ; Ribosomes/*enzymology ; Sequence Alignment
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 6
    Publication Date: 2007-11-10
    Description: Variants in the FTO (fat mass and obesity associated) gene are associated with increased body mass index in humans. Here, we show by bioinformatics analysis that FTO shares sequence motifs with Fe(II)- and 2-oxoglutarate-dependent oxygenases. We find that recombinant murine Fto catalyzes the Fe(II)- and 2OG-dependent demethylation of 3-methylthymine in single-stranded DNA, with concomitant production of succinate, formaldehyde, and carbon dioxide. Consistent with a potential role in nucleic acid demethylation, Fto localizes to the nucleus in transfected cells. Studies of wild-type mice indicate that Fto messenger RNA (mRNA) is most abundant in the brain, particularly in hypothalamic nuclei governing energy balance, and that Fto mRNA levels in the arcuate nucleus are regulated by feeding and fasting. Studies can now be directed toward determining the physiologically relevant FTO substrate and how nucleic acid methylation status is linked to increased fat mass.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2668859/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2668859/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Gerken, Thomas -- Girard, Christophe A -- Tung, Yi-Chun Loraine -- Webby, Celia J -- Saudek, Vladimir -- Hewitson, Kirsty S -- Yeo, Giles S H -- McDonough, Michael A -- Cunliffe, Sharon -- McNeill, Luke A -- Galvanovskis, Juris -- Rorsman, Patrik -- Robins, Peter -- Prieur, Xavier -- Coll, Anthony P -- Ma, Marcella -- Jovanovic, Zorica -- Farooqi, I Sadaf -- Sedgwick, Barbara -- Barroso, Ines -- Lindahl, Tomas -- Ponting, Chris P -- Ashcroft, Frances M -- O'Rahilly, Stephen -- Schofield, Christopher J -- 068086/Wellcome Trust/United Kingdom -- 077016/Wellcome Trust/United Kingdom -- G108/617/Medical Research Council/United Kingdom -- G9824984/Medical Research Council/United Kingdom -- MC_U137761446/Medical Research Council/United Kingdom -- U54 GM064346/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2007 Nov 30;318(5855):1469-72. Epub 2007 Nov 8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, Oxon OX1 3TA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17991826" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; Brain/enzymology/metabolism ; Cell Nucleus/enzymology ; Computational Biology ; DNA/*metabolism ; DNA Methylation ; DNA, Single-Stranded/metabolism ; Eating ; Energy Metabolism ; Fasting ; Ferrous Compounds/metabolism ; Hypothalamus/enzymology/metabolism ; Ketoglutaric Acids/*metabolism ; Male ; Mice ; Mixed Function Oxygenases ; Molecular Sequence Data ; Oxo-Acid-Lyases/chemistry/*genetics/*metabolism ; RNA, Messenger/genetics/metabolism ; Recombinant Proteins/metabolism ; Succinic Acid/metabolism ; Thymine/analogs & derivatives/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 7
    Publication Date: 2009-07-04
    Description: The finding that the metazoan hypoxic response is regulated by oxygen-dependent posttranslational hydroxylations, which regulate the activity and lifetime of hypoxia-inducible factor (HIF), has raised the question of whether other hydroxylases are involved in the regulation of gene expression. We reveal that the splicing factor U2 small nuclear ribonucleoprotein auxiliary factor 65-kilodalton subunit (U2AF65) undergoes posttranslational lysyl-5-hydroxylation catalyzed by the Fe(II) and 2-oxoglutarate-dependent dioxygenase Jumonji domain-6 protein (Jmjd6). Jmjd6 is a nuclear protein that has an important role in vertebrate development and is a human homolog of the HIF asparaginyl-hydroxylase. Jmjd6 is shown to change alternative RNA splicing of some, but not all, of the endogenous and reporter genes, supporting a specific role for Jmjd6 in the regulation of RNA splicing.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Webby, Celia J -- Wolf, Alexander -- Gromak, Natalia -- Dreger, Mathias -- Kramer, Holger -- Kessler, Benedikt -- Nielsen, Michael L -- Schmitz, Corinna -- Butler, Danica S -- Yates, John R 3rd -- Delahunty, Claire M -- Hahn, Phillip -- Lengeling, Andreas -- Mann, Matthias -- Proudfoot, Nicholas J -- Schofield, Christopher J -- Bottger, Angelika -- 084655/Wellcome Trust/United Kingdom -- G9826944/Medical Research Council/United Kingdom -- Biotechnology and Biological Sciences Research Council/United Kingdom -- Wellcome Trust/United Kingdom -- New York, N.Y. -- Science. 2009 Jul 3;325(5936):90-3. doi: 10.1126/science.1175865.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Chemistry Research Laboratory and Oxford Centre for Integrative Systems Biology, University of Oxford, 12 Mansfield Road, Oxford, Oxon OX1 3TA, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19574390" target="_blank"〉PubMed〈/a〉
    Keywords: *Alternative Splicing ; Amino Acid Sequence ; Biocatalysis ; Cell Line ; Chromatography, Liquid ; HeLa Cells ; Humans ; Hydroxylation ; Jumonji Domain-Containing Histone Demethylases ; Lysine/metabolism ; Molecular Sequence Data ; Nuclear Proteins/chemistry/*metabolism ; Protein Processing, Post-Translational ; RNA, Small Interfering ; Receptors, Cell Surface/genetics/*metabolism ; Recombinant Proteins/metabolism ; Ribonucleoproteins/chemistry/*metabolism ; Tandem Mass Spectrometry ; Tropomyosin/genetics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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