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  • 1
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    Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 A resolution (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publikationsdatum: 1995-04-28
    Beschreibung: The three-dimensional structure of the proteasome from the archaebacterium Thermoplasma acidophilum has been elucidated by x-ray crystallographic analysis by means of isomorphous replacement and cyclic averaging. The atomic model was built and refined to a crystallographic R factor of 22.1 percent. The 673-kilodalton protease complex consists of 14 copies of two different subunits, alpha and beta, forming a barrel-shaped structure of four stacked rings. The two inner rings consist of seven beta subunits each, and the two outer rings consist of seven alpha subunits each. A narrow channel controls access to the three inner compartments. The alpha 7 beta 7 beta 7 alpha 7 subunit assembly has 72-point group symmetry. The structures of the alpha and beta subunits are similar, consisting of a core of two antiparallel beta sheets that is flanked by alpha helices on both sides. The binding of a peptide aldehyde inhibitor marks the active site in the central cavity at the amino termini of the beta subunits and suggests a novel proteolytic mechanism.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lowe, J -- Stock, D -- Jap, B -- Zwickl, P -- Baumeister, W -- Huber, R -- New York, N.Y. -- Science. 1995 Apr 28;268(5210):533-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max-Planck-Institut fur Biochemie, Abteilung fur Strukturforschung, Martinsried, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7725097" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Amino Acid Sequence ; Archaeal Proteins ; Binding Sites ; Chaperonin 60/chemistry ; Computer Graphics ; Crystallography, X-Ray ; Cysteine Endopeptidases/*chemistry/metabolism ; Endopeptidases/*chemistry/metabolism ; Fourier Analysis ; Hydrogen Bonding ; Leupeptins/chemistry/metabolism ; *Models, Molecular ; Molecular Sequence Data ; Multienzyme Complexes/*chemistry/metabolism ; Protease Inhibitors/chemistry/metabolism ; Proteasome Endopeptidase Complex ; Protein Conformation ; Protein Folding ; Protein Structure, Secondary ; Proteins/metabolism ; Thermoplasma/*enzymology
    Print ISSN: 0036-8075
    Digitale ISSN: 1095-9203
    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Publiziert von American Association for the Advancement of Science (AAAS)
    Standort Signatur Erwartet Verfügbarkeit
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  • 2
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    Proteasome from Thermoplasma acidophilum: a threonine protease (1995)
    American Association for the Advancement of Science (AAAS)
    Details
    Publikationsdatum: 1995-04-28
    Beschreibung: The catalytic mechanism of the 20S proteasome from the archaebacterium Thermoplasma acidophilum has been analyzed by site-directed mutagenesis of the beta subunit and by inhibitor studies. Deletion of the amino-terminal threonine or its mutation to alanine led to inactivation of the enzyme. Mutation of the residue to serine led to a fully active enzyme, which was over ten times more sensitive to the serine protease inhibitor 3,4-dichloroisocoumarin. In combination with the crystal structure of a proteasome-inhibitor complex, the data show that the nucleophilic attack is mediated by the amino-terminal threonine of processed beta subunits. The conservation pattern of this residue in eukaryotic sequences suggests that at least three of the seven eukaryotic beta-type subunit branches should be proteolytically inactive.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Seemuller, E -- Lupas, A -- Stock, D -- Lowe, J -- Huber, R -- Baumeister, W -- New York, N.Y. -- Science. 1995 Apr 28;268(5210):579-82.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Abteilung fur Strukturbiologie Max-Planck Institut fur Biochemie, Martinsried, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/7725107" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Amino Acid Sequence ; Archaeal Proteins ; Binding Sites ; Coumarins/pharmacology ; Endopeptidases/*chemistry/metabolism ; Hydrogen-Ion Concentration ; Molecular Sequence Data ; Mutagenesis ; Protein Folding ; Sequence Alignment ; Serine Proteinase Inhibitors/pharmacology ; Thermoplasma/*enzymology
    Print ISSN: 0036-8075
    Digitale ISSN: 1095-9203
    Thema: Biologie , Chemie und Pharmazie , Informatik , Medizin , Allgemeine Naturwissenschaft , Physik
    Publiziert von American Association for the Advancement of Science (AAAS)
    Standort Signatur Erwartet Verfügbarkeit
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  • 3
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    Structure of transcribing mammalian RNA polymerase II (2016)
    Nature Publishing Group (NPG)
    Details
    Publikationsdatum: 2016-01-21
    Beschreibung: RNA polymerase (Pol) II produces messenger RNA during transcription of protein-coding genes in all eukaryotic cells. The Pol II structure is known at high resolution from X-ray crystallography for two yeast species. Structural studies of mammalian Pol II, however, remain limited to low-resolution electron microscopy analysis of human Pol II and its complexes with various proteins. Here we report the 3.4 A resolution cryo-electron microscopy structure of mammalian Pol II in the form of a transcribing complex comprising DNA template and RNA transcript. We use bovine Pol II, which is identical to the human enzyme except for seven amino-acid residues. The obtained atomic model closely resembles its yeast counterpart, but also reveals unknown features. Binding of nucleic acids to the polymerase involves 'induced fit' of the mobile Pol II clamp and active centre region. DNA downstream of the transcription bubble contacts a conserved 'TPSA motif' in the jaw domain of the Pol II subunit RPB5, an interaction that is apparently already established during transcription initiation. Upstream DNA emanates from the active centre cleft at an angle of approximately 105 degrees with respect to downstream DNA. This position of upstream DNA allows for binding of the general transcription elongation factor DSIF (SPT4-SPT5) that we localize over the active centre cleft in a conserved position on the clamp domain of Pol II. Our results define the structure of mammalian Pol II in its functional state, indicate that previous crystallographic analysis of yeast Pol II is relevant for understanding gene transcription in all eukaryotes, and provide a starting point for a mechanistic analysis of human transcription.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Bernecky, Carrie -- Herzog, Franz -- Baumeister, Wolfgang -- Plitzko, Jurgen M -- Cramer, Patrick -- England -- Nature. 2016 Jan 28;529(7587):551-4. doi: 10.1038/nature16482. Epub 2016 Jan 20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Gottingen, Germany. ; Gene Center Munich, Ludwig-Maximilians-Universitat Munchen, Feodor-Lynen-Strasse 25, 81377 Munich, Germany. ; Max Planck Institute for Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26789250" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Allosteric Regulation ; Amino Acid Motifs ; Animals ; Catalytic Domain ; Cattle ; *Cryoelectron Microscopy ; DNA/genetics/metabolism/ultrastructure ; Humans ; Models, Molecular ; Nucleic Acids/chemistry/metabolism ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; RNA Polymerase II/chemistry/*metabolism/*ultrastructure ; RNA, Messenger/biosynthesis/genetics/ultrastructure ; Saccharomyces cerevisiae/enzymology ; Templates, Genetic ; *Transcription Elongation, Genetic
    Print ISSN: 0028-0836
    Digitale ISSN: 1476-4687
    Thema: Biologie , Chemie und Pharmazie , Medizin , Allgemeine Naturwissenschaft , Physik
    Publiziert von Nature Publishing Group (NPG)
    Standort Signatur Erwartet Verfügbarkeit
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  • 4
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    Architecture of the RNA polymerase II-Mediator core initiation complex (2015)
    Nature Publishing Group (NPG)
    Details
    Publikationsdatum: 2015-02-06
    Beschreibung: The conserved co-activator complex Mediator enables regulated transcription initiation by RNA polymerase (Pol) II. Here we reconstitute an active 15-subunit core Mediator (cMed) comprising all essential Mediator subunits from Saccharomyces cerevisiae. The cryo-electron microscopic structure of cMed bound to a core initiation complex was determined at 9.7 A resolution. cMed binds Pol II around the Rpb4-Rpb7 stalk near the carboxy-terminal domain (CTD). The Mediator head module binds the Pol II dock and the TFIIB ribbon and stabilizes the initiation complex. The Mediator middle module extends to the Pol II foot with a 'plank' that may influence polymerase conformation. The Mediator subunit Med14 forms a 'beam' between the head and middle modules and connects to the tail module that is predicted to bind transcription activators located on upstream DNA. The Mediator 'arm' and 'hook' domains contribute to a 'cradle' that may position the CTD and TFIIH kinase to stimulate Pol II phosphorylation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Plaschka, C -- Lariviere, L -- Wenzeck, L -- Seizl, M -- Hemann, M -- Tegunov, D -- Petrotchenko, E V -- Borchers, C H -- Baumeister, W -- Herzog, F -- Villa, E -- Cramer, P -- England -- Nature. 2015 Feb 19;518(7539):376-80. doi: 10.1038/nature14229. Epub 2015 Feb 4.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Fassberg 11, 37077 Gottingen, Germany. ; Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universitat Munchen, Feodor-Lynen-Strasse 25, 81377 Munich, Germany. ; Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany. ; Department of Biochemistry and Microbiology, Genome British Columbia Protein Centre, University of Victoria, 3101-4464 Markham Street, Victoria, British Columbia V8Z7X8, Canada. ; 1] Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany [2] Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25652824" target="_blank"〉PubMed〈/a〉
    Schlagwort(e): Allosteric Regulation ; Binding Sites ; *Cryoelectron Microscopy ; DNA/chemistry/metabolism ; Enzyme Activation ; Mediator Complex/*chemistry/metabolism/*ultrastructure ; Models, Molecular ; Phosphorylation ; Protein Stability ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; RNA Polymerase II/*chemistry/metabolism/*ultrastructure ; Saccharomyces cerevisiae/*chemistry/*ultrastructure ; Saccharomyces cerevisiae Proteins/chemistry/metabolism/ultrastructure ; Transcription Factor TFIIB/chemistry/metabolism ; Transcription Factor TFIIH/chemistry/metabolism ; Transcription Initiation, Genetic
    Print ISSN: 0028-0836
    Digitale ISSN: 1476-4687
    Thema: Biologie , Chemie und Pharmazie , Medizin , Allgemeine Naturwissenschaft , Physik
    Publiziert von Nature Publishing Group (NPG)
    Standort Signatur Erwartet Verfügbarkeit
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