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  • 1
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    RNA degradation paths in a 12-subunit nuclear exosome complex (2015)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2015-07-30
    Description: The eukaryotic exosome is a conserved RNA-degrading complex that functions in RNA surveillance, turnover and processing. How the same machinery can either completely degrade or precisely trim RNA substrates has long remained unexplained. Here we report the crystal structures of a yeast nuclear exosome containing the 9-subunit core, the 3'-5' RNases Rrp44 and Rrp6, and the obligate Rrp6-binding partner Rrp47 in complex with different RNAs. The combined structural and biochemical data of this 12-subunit complex reveal how a single-stranded RNA can reach the Rrp44 or Rrp6 active sites directly or can bind Rrp6 and be threaded via the central channel towards the distal RNase Rrp44. When a bulky RNA is stalled at the entrance of the channel, Rrp6-Rrp47 swings open. The results suggest how the same molecular machine can coordinate processive degradation and partial trimming in an RNA-dependent manner by a concerted swinging mechanism of the two RNase subunits.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Makino, Debora Lika -- Schuch, Benjamin -- Stegmann, Elisabeth -- Baumgartner, Marc -- Basquin, Claire -- Conti, Elena -- England -- Nature. 2015 Aug 6;524(7563):54-8. doi: 10.1038/nature14865. Epub 2015 Jul 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Cell Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26222026" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    How a DNA polymerase clamp loader opens a sliding clamp (2011)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2011-12-24
    Description: Processive chromosomal replication relies on sliding DNA clamps, which are loaded onto DNA by pentameric clamp loader complexes belonging to the AAA+ family of adenosine triphosphatases (ATPases). We present structures for the ATP-bound state of the clamp loader complex from bacteriophage T4, bound to an open clamp and primer-template DNA. The clamp loader traps a spiral conformation of the open clamp so that both the loader and the clamp match the helical symmetry of DNA. One structure reveals that ATP has been hydrolyzed in one subunit and suggests that clamp closure and ejection of the loader involves disruption of the ATP-dependent match in symmetry. The structures explain how synergy among the loader, the clamp, and DNA can trigger ATP hydrolysis and release of the closed clamp on DNA.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3281585/" 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/PMC3281585/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kelch, Brian A -- Makino, Debora L -- O'Donnell, Mike -- Kuriyan, John -- F32 GM087888/GM/NIGMS NIH HHS/ -- F32 GM087888-02/GM/NIGMS NIH HHS/ -- F32-087888/PHS HHS/ -- R01 GM038839/GM/NIGMS NIH HHS/ -- R01 GM038839-26/GM/NIGMS NIH HHS/ -- R01 GM045547/GM/NIGMS NIH HHS/ -- R01 GM045547-20/GM/NIGMS NIH HHS/ -- R01-GM308839/GM/NIGMS NIH HHS/ -- R01-GM45547/GM/NIGMS NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2011 Dec 23;334(6063):1675-80. doi: 10.1126/science.1211884.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22194570" target="_blank"〉PubMed〈/a〉
    Keywords: Adenosine Triphosphatases/*chemistry/metabolism ; Adenosine Triphosphate/metabolism ; Bacteriophage T4 ; Binding Sites ; Crystallography, X-Ray ; DNA, A-Form/*chemistry/metabolism ; DNA, Viral/*chemistry/metabolism ; DNA-Directed DNA Polymerase/chemistry/*metabolism ; Hydrolysis ; Models, Molecular ; Nucleic Acid Conformation ; Protein Conformation ; Protein Structure, Tertiary ; Protein Subunits/chemistry/metabolism ; Static Electricity ; Templates, Genetic ; Trans-Activators/*chemistry/metabolism ; Viral Proteins/*chemistry/metabolism
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
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    Crystal structure of an RNA-bound 11-subunit eukaryotic exosome complex (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-02-05
    Description: The exosome is the major 3'-5' RNA-degradation complex in eukaryotes. The ubiquitous core of the yeast exosome (Exo-10) is formed by nine catalytically inert subunits (Exo-9) and a single active RNase, Rrp44. In the nucleus, the Exo-10 core recruits another nuclease, Rrp6. Here we crystallized an approximately 440-kilodalton complex of Saccharomyces cerevisiae Exo-10 bound to a carboxy-terminal region of Rrp6 and to an RNA duplex with a 3'-overhang of 31 ribonucleotides. The 2.8 A resolution structure shows how RNA is funnelled into the Exo-9 channel in a single-stranded conformation by an unwinding pore. Rrp44 adopts a closed conformation and captures the RNA 3'-end that exits from the side of Exo-9. Exo-9 subunits bind RNA with sequence-unspecific interactions reminiscent of archaeal exosomes. The substrate binding and channelling mechanisms of 3'-5' RNA degradation complexes are conserved in all kingdoms of life.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Makino, Debora Lika -- Baumgartner, Marc -- Conti, Elena -- England -- Nature. 2013 Mar 7;495(7439):70-5. doi: 10.1038/nature11870. Epub 2013 Feb 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Structural Cell Biology, MPI for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23376952" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Exosome Multienzyme Ribonuclease Complex/*chemistry/*metabolism ; Models, Molecular ; Protein Subunits/*chemistry/metabolism ; RNA/chemistry/*metabolism ; Saccharomyces cerevisiae/*chemistry/genetics ; Saccharomyces cerevisiae Proteins/*chemistry/*metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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