Structural analysis of mtEXO mitochondrial RNA degradosome reveals tight coupling of nuclease and helicase components

[1]  E. Hurt,et al.  Structural insights into the interaction of the nuclear exosome helicase Mtr4 with the preribosomal protein Nop53 , 2017, RNA.

[2]  L. Joshua-Tor,et al.  Multi-domain utilization by TUT4 and TUT7 in control of let-7 biogenesis , 2017, Nature Structural &Molecular Biology.

[3]  A. Dziembowski,et al.  Perlman syndrome nuclease DIS3L2 controls cytoplasmic non-coding RNAs and provides surveillance pathway for maturing snRNAs , 2016, Nucleic acids research.

[4]  Andrej Sali,et al.  FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles , 2016, Nucleic Acids Res..

[5]  N. Pavletich,et al.  Dna2 nuclease-helicase structure, mechanism and regulation by Rpa , 2015, eLife.

[6]  V. Sperandio,et al.  Structural and Mechanistic Roles of Novel Chemical Ligands on the SdiA Quorum-Sensing Transcription Regulator , 2015, mBio.

[7]  Rongguang Zhang,et al.  Structures of CRISPR Cas3 offer mechanistic insights into Cascade-activated DNA unwinding and degradation , 2014, Nature Structural &Molecular Biology.

[8]  L. Joshua-Tor,et al.  Mechanism of Dis3L2 substrate recognition in the Lin28/let-7 pathway , 2014, Nature.

[9]  Marco Biasini,et al.  SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information , 2014, Nucleic Acids Res..

[10]  M. Rode,et al.  The Yeast Ski Complex: Crystal Structure and RNA Channeling to the Exosome Complex , 2013, Cell.

[11]  Philip R. Evans,et al.  How good are my data and what is the resolution? , 2013, Acta crystallographica. Section D, Biological crystallography.

[12]  P. Stepien,et al.  Human mitochondrial RNA decay mediated by PNPase–hSuv3 complex takes place in distinct foci , 2012, Nucleic acids research.

[13]  D. Wigley.  Bacterial DNA repair: recent insights into the mechanism of RecBCD, AddAB and AdnAB , 2012, Nature Reviews Microbiology.

[14]  S. Boulton,et al.  Playing the end game: DNA double-strand break repair pathway choice. , 2012, Molecular cell.

[15]  Michael Krug,et al.  XDSAPP: a graphical user interface for the convenient processing of diffraction data using XDS , 2012 .

[16]  Sung Gyun Kang,et al.  One-Step Sequence- and Ligation-Independent Cloning as a Rapid and Versatile Cloning Method for Functional Genomics Studies , 2012, Applied and Environmental Microbiology.

[17]  Pick-Wei Lau,et al.  The Molecular Architecture of Human Dicer , 2012, Nature Structural &Molecular Biology.

[18]  J. Hunt,et al.  The structure and enzymatic properties of a novel RNase II family enzyme from Deinococcus radiodurans. , 2012, Journal of molecular biology.

[19]  M. Teichmann,et al.  Structural and functional aspects of winged-helix domains at the core of transcription initiation complexes , 2012, Transcription.

[20]  Z. Dauter,et al.  Human Suv3 protein reveals unique features among SF2 helicases. , 2011, Acta crystallographica. Section D, Biological crystallography.

[21]  Randy J. Read,et al.  Overview of the CCP4 suite and current developments , 2011, Acta crystallographica. Section D, Biological crystallography.

[22]  Liisa Holm,et al.  Dali server: conservation mapping in 3D , 2010, Nucleic Acids Res..

[23]  P. Emsley,et al.  Features and development of Coot , 2010, Acta crystallographica. Section D, Biological crystallography.

[24]  F. Gebauer,et al.  Eukaryotic cold shock domain proteins: highly versatile regulators of gene expression , 2010, BioEssays : news and reviews in molecular, cellular and developmental biology.

[25]  Randy J. Read,et al.  Acta Crystallographica Section D Biological , 2003 .

[26]  Charles M. Rice,et al.  Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism , 2009, Proceedings of the National Academy of Sciences.

[27]  Vincent B. Chen,et al.  Correspondence e-mail: , 2000 .

[28]  F. Bonneau,et al.  The Yeast Exosome Functions as a Macromolecular Cage to Channel RNA Substrates for Degradation , 2009, Cell.

[29]  Phang-lang Chen,et al.  Human Mitochondrial SUV3 and Polynucleotide Phosphorylase Form a 330-kDa Heteropentamer to Cooperatively Degrade Double-stranded RNA with a 3′-to-5′ Directionality* , 2009, The Journal of Biological Chemistry.

[30]  Greg L. Hura,et al.  Structure and flexibility within proteins as identified through small angle X-ray scattering. , 2009, General physiology and biophysics.

[31]  P. Gómez-Puertas,et al.  Determination of Key Residues for Catalysis and RNA Cleavage Specificity , 2009, The Journal of Biological Chemistry.

[32]  D. Tollervey,et al.  The Many Pathways of RNA Degradation , 2009, Cell.

[33]  E. Conti,et al.  Structure of the active subunit of the yeast exosome core, Rrp44: diverse modes of substrate recruitment in the RNase II nuclease family. , 2008, Molecular cell.

[34]  P. Golik,et al.  In vitro reconstitution and characterization of the yeast mitochondrial degradosome complex unravels tight functional interdependence. , 2007, Journal of molecular biology.

[35]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[36]  M. A. Carrondo,et al.  Unravelling the dynamics of RNA degradation by ribonuclease II and its RNA-bound complex , 2006, Nature.

[37]  A. Fialho,et al.  Characterization of the functional domains of Escherichia coli RNase II. , 2006, Journal of molecular biology.

[38]  L. Aravind,et al.  The many faces of the helix-turn-helix domain: transcription regulation and beyond. , 2005, FEMS microbiology reviews.

[39]  M. Minczuk,et al.  RNA Degradation in Yeast and Human Mitochondria , 2004, Toxicology mechanisms and methods.

[40]  Dmitri I. Svergun,et al.  PRIMUS: a Windows PC-based system for small-angle scattering data analysis , 2003 .

[41]  Dmitri I. Svergun,et al.  Uniqueness of ab initio shape determination in small-angle scattering , 2003 .

[42]  L. Grivell,et al.  The Yeast Mitochondrial Degradosome , 2003, The Journal of Biological Chemistry.

[43]  B. Dujon,et al.  The complete mitochondrial genome sequence of the pathogenic yeast Candida (Torulopsis) glabrata , 2003, FEBS letters.

[44]  Huilin Li,et al.  Phosphorylation is required for high-affinity binding of DBP, a yeast mitochondrial site-specific RNA binding protein , 2000, Current Genetics.

[45]  D I Svergun,et al.  Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing. , 1999, Biophysical journal.

[46]  Mian Is,et al.  Comparative sequence analysis of ribonucleases HII, III, II PH and D. , 1997 .

[47]  Mark Proctor,et al.  The Solution Structure of the S1 RNA Binding Domain: A Member of an Ancient Nucleic Acid–Binding Fold , 1997, Cell.

[48]  C. Ouzounis,et al.  KOW: a novel motif linking a bacterial transcription factor with ribosomal proteins. , 1996, Trends in biochemical sciences.

[49]  R. A. Butow,et al.  RNA turnover and the control of mitochondrial gene expression. , 1996, Trends in biochemical sciences.

[50]  T. Blundell,et al.  Comparative protein modelling by satisfaction of spatial restraints. , 1993, Journal of molecular biology.

[51]  M. Suzuki.  Common features in DNA recognition helices of eukaryotic transcription factors. , 1993, The EMBO journal.

[52]  J. Min,et al.  Isolation and characterization of an NTP-dependent 3'-exoribonuclease from mitochondria of Saccharomyces cerevisiae. , 1993, The Journal of biological chemistry.

[53]  D. Svergun,et al.  Synchrotron radiation solution X-ray scattering study of the pH dependence of the quaternary structure of yeast pyruvate decarboxylase. , 1992, Biochemistry.

[54]  R. D. Gietz,et al.  New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. , 1988, Gene.

[55]  M. Sattler,et al.  Structural insights into the interaction of the nuclear exosome helicase Mtr4 with the pre-ribosomal protein Nop53 , 2017 .

[56]  M. Rode,et al.  The crystal structure of S. cerevisiae Ski2, a DExH helicase associated with the cytoplasmic functions of the exosome. , 2012, RNA.

[57]  P. Golik,et al.  In vivo and in vitro approaches for studying the yeast mitochondrial RNA degradosome complex. , 2008, Methods in enzymology.

[58]  I. Mian.  Comparative sequence analysis of ribonucleases HII, III, II PH and D. , 1997, Nucleic acids research.