Udo Oppermann

University of Oxford, Oxford, England, United Kingdom

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Publications (188)1007.18 Total impact

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    ABSTRACT: The Structural Genomics Consortium (SGC) and its clinical, industry and disease-foundation partners are launching open-source preclinical translational medicine studies.
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    ABSTRACT: Dentine matrix protein 1 (DMP-1) is a non-collagenous matrix protein found in dentine and bone. It is highly expressed by osteocytes and has been identified in primary benign and malignant osteogenic bone tumours. Bone formation and matrix mineralisation are seen in a variety of benign and malignant soft tissue tumours and tumour-like lesions, and in this study, we analysed immunohistochemically the DMP-1 expression in a wide range of soft tissue lesions (n = 254) in order to assess whether DMP-1 expression is useful in the histological diagnosis of soft tissue tumours. Matrix staining of DMP-1 was seen in all cases of myositis ossificans, fibro-osseous tumour of the digits, extraskeletal soft tissue osteosarcoma and in most cases of ossifying fibromyxoid tumour. DMP-1 was also noted in dense collagenous connective tissue of mineralising soft tissue lesions such as tumoural calcinosis, dermatomyositis and calcific tendinitis. DMP-1 was expressed in areas of focal ossification and calcification in synovial sarcoma and other soft tissue tumours. With few exceptions, DMP-1 was not expressed in other benign and malignant soft tissue tumours. Our findings indicate that DMP-1 is a matrix marker of bone formation and mineralisation in soft tissue tumours. DMP-1 expression should be particularly useful in distinguishing extraskeletal osteosarcoma and ossifying fibromyxoid tumour from other sarcomas and in identifying areas of osteoid/bone formation and mineralisation in soft tissue tumours.
    Archiv für Pathologische Anatomie und Physiologie und für Klinische Medicin 01/2015; DOI:10.1007/s00428-014-1706-3
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    ABSTRACT: Prostaglandins (PGs) are lipid compounds derived from arachidonic acid by the action of cyclooxygenases, acting locally as messenger molecules in a wide variety of physiological processes, such as inflammation, cell survival, apoptosis, smooth muscle contraction, adipocyte differentiation, vasodilation and platelet aggregation inhibition. In the inactivating pathway of PGs, the first metabolic intermediates are 15-keto-PGs, which are further converted into 13,14-dihydro-15-keto-PGs by different enzymes having 15-keto-PG reductase activity. Three human PG reductases (PGR), zinc-independent members of the medium-chain dehydrogenase/reductase (MDR) superfamily, perform the first irreversible step of the degradation pathway. We have focused on the characterization of the recombinant human enzyme prostaglandin reductase 1 (PGR1), also known as leukotriene B4 dehydrogenase. Only a partial characterization of this enzyme, isolated from human placenta, had been previously reported. In the present work, we have developed a new HPLC-based method for the determination of the 15-keto-PG reductase activity. We have performed an extensive kinetic characterization of PGR1, which catalyzes the NADPH-dependent reduction of α,β-double bond of aliphatic and aromatic aldehydes and ketones, and 15-keto-PGs. PGR1 also shows low activity in the oxidation of leukotriene B4. The best substrates in terms of kcat/Km were 15-keto-PGE2, trans-3-nonen-2-one and trans-2-decenal. Molecular docking simulations, based on the three-dimensional structure of the human enzyme (PDB ID 2Y05), and site-directed mutagenesis studies were performed to pinpoint important structural determinants, highlighting the role of Arg56 and Tyr245 in 15-keto-PG binding. Finally, inhibition analysis was done using non-steroidal anti-inflammatory drugs (NSAIDs) as potential inhibitors. Copyright © 2015. Published by Elsevier Ireland Ltd.
    Chemico-Biological Interactions 01/2015; 234. DOI:10.1016/j.cbi.2015.01.021
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    ABSTRACT: Short-chain dehydrogenases/reductases (SDRs) constitute a large, functionally diverse branch of enzymes within the class of NAD(P)(H) dependent oxidoreductases. In humans, over 80 genes have been identified with distinct metabolic roles in carbohydrate, amino acid, lipid, retinoid and steroid hormone metabolism, frequently associated with inherited genetic defects. Besides metabolic functions, a subset of atypical SDR proteins appears to play critical roles in adapting to redox status or RNA processing, and thereby controlling metabolic pathways.
    Chemico-Biological Interactions 12/2014; 234. DOI:10.1016/j.cbi.2014.12.013
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    ABSTRACT: Osteoclasts are specialised bone resorbing cells which form by fusion of circulating mononuclear phagocyte precursors. Bone resorption results in the release of large amounts of calcium into the extracellular fluid (ECF), but it is not certain whether changes in extracellular calcium concentration [Ca(2+)]e influence osteoclast formation and resorption. In this study, we sought to determine the effect of [Ca(2+)]e and NAADP, a potent calcium mobilising messenger that induces calcium uptake, on human osteoclast formation and resorption. CD14+ human monocytes were cultured with M-CSF and RANKL in the presence of different concentrations of calcium and NAADP and the effect on osteoclast formation and resorption evaluated. We found that the number of TRAP+ multinucleated cells and the extent of lacunar resorption were reduced when there was an increase in extracellular calcium and NAADP. This was associated with a decrease in RANK mRNA expression by CD14+ cells. At high concentrations (20 mM) of [Ca(2+)]e mature osteoclast resorption activity remained unaltered relative to control cultures. Our findings indicate that osteoclast formation is inhibited by a rise in [Ca(2+)]e and that RANK expression by mononuclear phagocyte osteoclast precursors is also [Ca(2+)]e dependent. Changes in NAADP also influence osteoclast formation, suggesting a role for this molecule in calcium handling. Osteoclasts remained capable of lacunar resorption, even at high ECF [Ca(2+)]e, in keeping with their role in physiological and pathological bone resorption.
    Calcified Tissue International 11/2014; 96(1). DOI:10.1007/s00223-014-9939-3
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    ABSTRACT: Replying to B. Heinemann . Nature 514, http://dx.doi.org/10.1038/nature13688 (2014)We welcome the accompanying Comment by Heinemann et al., in which the authors use an extensive panel of sensitive KDM assays to independently confirm our results that GSK-J1 is a potent KDM6 inhibitor. Additionally, Heinemann et al. demonstrate that GSK-J1 has some, albeit weaker, activity towards KDM5B and KDM5C, for which we only had preliminary data available at the time of our original publication. As our jumonji assay portfolio expands, we have continued to update the GSK-J1 activity profile on the SGC website (http://www.thesgc.org/chemical-probes/GSKJ1); this includes KDM5 inhibition activity by GSK-J1 similar to that reported by Heinemann. In conclusion, GSK-J1 remains the most selective KDM inhibitor yet disclosed and thus a valuable chemical tool.
    Nature 10/2014; 514(7520):E2. DOI:10.1038/nature13689
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    ABSTRACT: The retinoblastoma tumor suppressor protein pRb is a key regulator of cell cycle progression and mediator of the DNA damage response. Lysine methylation at K810, which occurs within a critical Cdk phosphorylation motif, holds pRb in the hypophosphorylated growth-suppressing state. We show here that methyl K810 is read by the tandem tudor domain containing tumor protein p53 binding protein 1 (53BP1). Structural elucidation of 53BP1 in complex with a methylated K810 pRb peptide emphasized the role of the 53BP1 tandem tudor domain in recognition of the methylated lysine and surrounding residues. Significantly, binding of 53BP1 to methyl K810 occurs on E2 promoter binding factor target genes and allows pRb activity to be effectively integrated with the DNA damage response. Our results widen the repertoire of cellular targets for 53BP1 and suggest a previously unidentified role for 53BP1 in regulating pRb tumor suppressor activity.
    Proceedings of the National Academy of Sciences 07/2014; 111(31). DOI:10.1073/pnas.1403737111
  • Annals of the Rheumatic Diseases 06/2014; 73(Suppl 2):823-824. DOI:10.1136/annrheumdis-2014-eular.4218
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    ABSTRACT: 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(ε)-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.
    Nature 05/2014; 510(7505). DOI:10.1038/nature13263
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    ABSTRACT: The Jumonji C lysine demethylases (KDMs) are 2-oxoglutarate and Fe(II) dependent oxygenases. KDM6A (UTX) and KDM6B (JMJD3) are KDM6 subfamily members which catalyse demethylation of Nε-methylated histone 3 lysine-27 (H3K27), a mark important for transcriptional repression. Despite reports stating that UTY(KDM6C) is inactive as a KDM, we demonstrate by biochemical studies, employing mass spectrometry and NMR, that UTY(KDM6C) is an active KDM. Crystallographic analyses reveal that the UTY(KDM6C) active site is highly conserved with those of KDM6B and KDM6A. UTY(KDM6C) catalyses demethylation of H3K27 peptides in vitro, analogously to KDM6B and KDM6A, but with reduced activity, due to point substitutions involved in substrate binding. The results expand the set of human KDMs and will be of use in developing selective KDM inhibitors.
    Journal of Biological Chemistry 05/2014; 289(26). DOI:10.1074/jbc.M114.555052
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    ABSTRACT: The iron- and 2-oxoglutarate-dependent oxygenases constitute a phylogenetically conserved class of enzymes that catalyze hydroxylation reactions in humans by acting on various types of substrates, including metabolic intermediates, amino acid residues in different proteins and various types of nucleic acids. The discovery of jumonji (Jmj), the founding member of a class of Jmj-type chromatin modifying enzymes and transcriptional regulators, has culminated in the discovery of several branches of histone lysine demethylases, with essential functions in regulating the epigenetic landscape of the chromatin environment. This work has now been considerably expanded into other aspects of epigenetic biology and includes the discovery of enzymatic steps required for methyl-cytosine demethylation as well as modification of RNA and ribosomal proteins. This overview aims to summarize the current knowledge on the human Jmj-type enzymes and their involvement in human pathological processes, including development, cancer, inflammation and metabolic diseases.
    Epigenomics 02/2014; 6(1):89-120. DOI:10.2217/epi.13.79
  • Spring Meeting of the British-Society-for-Matrix-Biology; 10/2013
  • S Munro, U Oppermann, N B La Thangue
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    ABSTRACT: Transcription factor E2F-1 and its interaction with pRb provide a key point of control in cell proliferation. E2F-1 participates in both cell cycle progression and apoptosis, and in cells exists with a DP dimerization partner protein, the most prominent being DP-1. By mining the tumor tissue and cancer cell line encyclopedia genomic databases, we identified the first somatic mutations in the DP-1 gene and describe 53 distinct mutation events here. The mutations are mostly missense mutations, but also include nonsense and frame-shift mutations that result in truncated DP-1 derivatives. Mutation occurs throughout the DP-1 gene but generally leaves protein dimerization activity intact. This allows the mutant derivatives to affect the properties of the E2F-1/DP-1 heterodimer through a transdominant mechanism, which changes the DNA binding, transcriptional activation and pRb-binding properties of the heterodimer. In particular, many DP-1 mutants were found to impair E2F-1-dependent apoptosis. Our results establish that somatic mutations in DP-1 uncouple normal control of the E2F pathway, and thus define a new mechanism that could contribute to aberrant proliferation in tumor cells.Oncogene advance online publication, 12 August 2013; doi:10.1038/onc.2013.316.
    Oncogene 08/2013; 33(27). DOI:10.1038/onc.2013.316
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    ABSTRACT: Malonyl-coenzyme A decarboxylase (MCD) is found from bacteria to humans, has important roles in regulating fatty acid metabolism and food intake, and is an attractive target for drug discovery. We report here four crystal structures of MCD from human, Rhodopseudomonas palustris, Agrobacterium vitis, and Cupriavidus metallidurans at up to 2.3 Å resolution. The MCD monomer contains an N-terminal helical domain involved in oligomerization and a C-terminal catalytic domain. The four structures exhibit substantial differences in the organization of the helical domains and, consequently, the oligomeric states and intersubunit interfaces. Unexpectedly, the MCD catalytic domain is structurally homologous to those of the GCN5-related N-acetyltransferase superfamily, especially the curacin A polyketide synthase catalytic module, with a conserved His-Ser/Thr dyad important for catalysis. Our structures, along with mutagenesis and kinetic studies, provide a molecular basis for understanding pathogenic mutations and catalysis, as well as a template for structure-based drug design.
    Structure 06/2013; DOI:10.1016/j.str.2013.05.001
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    ABSTRACT: ah 2-Oxoglutarate and iron dependent oxygenases are therapeutic targets for human diseases. Using a representative 2OG oxygenase panel, we compare the inhibitory activities of 5-carboxy-8-hydroxyquinoline (IOX1) and 4-carboxy-8-hydroxyquinoline (4C8HQ) with that of two other commonly used 2OG oxygenase inhibitors, N-oxalylglycine (NOG) and 2,4-pyridinedicarboxylic acid (2,4-PDCA). The results reveal that IOX1 has a broad spectrum of activity, as demonstrated by the inhibition of transcription factor hydroxylases, representatives of all 2OG dependent histone demethylase subfamilies, nucleic acid demethylases and g-butyrobetaine hydroxylase. Cellular assays show that, unlike NOG and 2,4-PDCA, IOX1 is active against both cytosolic and nuclear 2OG oxygenases without ester derivatisation. Unexpectedly, crystallographic studies on these oxygenases demonstrate that IOX1, but not 4C8HQ, can cause translocation of the active site metal, revealing a rare example of protein ligand-induced metal movement.
    Chemical Science 06/2013; 4(8):3110-3117. DOI:10.1039/c3sc51122g
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    ABSTRACT: We previously reported methylstat as a selective inhibitor of jumonji C domain-containing histone demethylases (JHDMs). Herein, we describe the synthesis of a fluorescent analogue of methylstat and its application as a tracer in fluorescence polarization assays. Using this format, we have evaluated the binding affinities of several known JHDM probes, as well as the native cofactor and substrate of JHDM1A. This fluorophore allowed a highly robust and miniaturized competition assay sufficient for high-throughput screening.
    Journal of Medicinal Chemistry 05/2013; 56(12). DOI:10.1021/jm3018628
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    ABSTRACT: Dentin matrix protein 1 (DMP-1) is highly expressed by osteocytes and is a non-collagenous matrix protein found in dentin and bone. In this study, we determined the expression of DMP-1 in mature and immature human bone and examined whether DMP-1 is useful in distinguishing osteoid/bone-forming tumours from other primary and secondary bone tumours. DMP-1 expression was immunohistochemically determined in paraffin sections of a wide range of benign and malignant primary bone tumours and tumour-like lesions (n = 353). DMP-1 mRNA expression was also examined in osteosarcoma and fibrosarcoma cell lines as well as bone tumour specimens (n = 5) using real-time PCR. In lamellar and woven bone, DMP-1 was expressed in the matrix around osteocyte lacunae and canaliculi; osteoblasts and other cell types in the bone were negative. Matrix staining of the osteoid and bone was seen in bone-forming tumours including osteoma, osteoid osteoma, osteoblastoma and osteosarcoma. DMP-1 staining was also seen in fibrous dysplasia, osteofibrous dysplasia and chondroblastoma and in reactive bone in solitary bone cysts and aneurysmal bone cysts. DMP-1 was not expressed in the tumour component of other bone neoplasms including Ewing sarcoma, chondrosarcoma, leiomyosarcoma, fibrosarcoma, giant cell tumour of bone and metastatic carcinoma. DMP-1 mRNA was expressed in osteosarcoma cell lines and tumour samples. DMP-1 is a matrix marker expressed around osteocytes in human woven and lamellar bone and is useful in identifying osteosarcoma and other bone-forming tumours.
    Archiv für Pathologische Anatomie und Physiologie und für Klinische Medicin 04/2013; 462(5). DOI:10.1007/s00428-013-1399-z
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    Udo Oppermann
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    ABSTRACT: In its widest sense, the term epigenetics describes a range of mechanisms in genome function that do not solely result from the DNA sequence itself. These mechanisms comprise DNA and chromatin modifications and their associated systems, as well as the noncoding RNA machinery. The epigenetic apparatus is essential for controlling normal development and homeostasis, and also provides a means for the organism to integrate and react upon environmental cues. A multitude of functional studies as well as systematic genome-wide mapping of epigenetic marks and chromatin modifiers reveal the importance of epigenomic mechanisms in human pathologies, including inflammatory conditions and musculoskeletal disease such as rheumatoid arthritis. Collectively, these studies pave the way to identify possible novel therapeutic intervention points and to investigate the utility of drugs that interfere with epigenetic signalling not only in cancer, but possibly also in inflammatory and autoimmune diseases.
    Arthritis research & therapy 04/2013; 15(2):209. DOI:10.1186/ar4186
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    ABSTRACT: Methionine adenosyltransferase (MAT) utilizes L-methionine and ATP to form S-adenosyl-l-methionine (SAM), the principal methyl donor in biological methylations. Mammals encode a liver-specific isozyme MAT1A that is genetically linked with an inborn metabolic disorder of hypermethioninemia, as well as a ubiquitously-expressed isozyme MAT2A whose enzymatic activity is regulated by an associated subunit MAT2B. To understand the molecular mechanism of MAT functions and interactions, we have crystallized the ligand-bound complexes of human MAT1A, MAT2A and MAT2B. The MAT1A and MAT2A structures in binary complexes with product SAM allow a comparison with the previous E. coli and rat structures, to understand the different substrate or product conformations, mediated by the neighbouring gating loop, which can be accommodated by the compact active site during catalysis. The structure of MAT2B reveals a short-chain dehydrogenase/reductase (SDR) core with specificity for the NADP/H cofactor, and harbours the SDR catalytic triad (Tyr-x-x-x-Lys, Ser). Extended from the MAT2B core is a second domain with homology to an SDR sub-family that binds nucleotide-sugar substrates, although the equivalent region in MAT2B presents a more open and extended surface which may endow a different ligand/protein-binding capability. Together, our data provide a framework to assign structural features to the functional and catalytic properties of the human MAT proteins, and facilitate future studies to probe new catalytic and binding functions.
    Biochemical Journal 02/2013; 452(Pt 1). DOI:10.1042/BJ20121580
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    ABSTRACT: Succinyl-CoA:3-ketoacid CoA transferase (SCOT) deficiency is a rare inherited metabolic disorder of ketone metabolism, characterized by ketoacidotic episodes and often permanent ketosis. To date there are ∼20 disease-associated alleles on the OXCT1 gene that encodes the mitochondrial enzyme SCOT. SCOT catalyzes the first, rate-limiting step of ketone body utilization in peripheral tissues, by transferring a CoA moiety from succinyl-CoA to form acetoacetyl-CoA, for entry into the tricarboxylic acid cycle for energy production. We have determined the crystal structure of human SCOT, providing a molecular understanding of the reported mutations based on their potential structural effects. An interactive version of this manuscript (which may contain additional mutations appended after acceptance of this manuscript) may be found on the web address: http://www.thesgc.org/jimd/SCOT .
    Journal of Inherited Metabolic Disease 02/2013; 36(6). DOI:10.1007/s10545-013-9589-z

Publication Stats

7k Citations
1,007.18 Total Impact Points

Institutions

  • 2007–2015
    • University of Oxford
      • Structural Genomics Consortium (SGC)
      Oxford, England, United Kingdom
  • 2008–2014
    • NIHR Oxford Biomedical Research
      Oxford, England, United Kingdom
  • 2011–2012
    • Graz University of Technology
      • Institut für Biotechnologie und Bioprozesstechnik
      Graz, Styria, Austria
    • University of Bristol
      • School of Biochemistry
      Bristol, England, United Kingdom
  • 2010
    • The University of Sheffield
      Sheffield, England, United Kingdom
  • 2009
    • National Human Genome Research Institute
      Maryland, United States
  • 1996–2008
    • Karolinska Institutet
      • Department of Medical Biochemistry and Biophysics
      Solna, Stockholm, Sweden
  • 1992–1993
    • Philipps University of Marburg
      • Institute for Physiological Chemistry
      Marburg, Hesse, Germany