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RNP disruption by the spliceosomal Brr2 helicase [Biochemistry] (2016)

Theuser, M., Hobartner, C., Wahl, M. C., Santos, K. F.

National Academy of Sciences

In: PNAS - Proceedings of the National Academy of Sciences

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Publication Date: 2016-07-13

Description: The Brr2 RNA helicase disrupts the U4/U6 di-small nuclear RNA–protein complex (di-snRNP) during spliceosome activation via ATP-driven translocation on the U4 snRNA strand. However, it is unclear how bound proteins influence U4/U6 unwinding, which regions of the U4/U6 duplex the helicase actively unwinds, and whether U4/U6 components are released as...

Print ISSN: 0027-8424

Electronic ISSN: 1091-6490

Topics: Biology , Medicine , Natural Sciences in General

Published by National Academy of Sciences

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Helical extension of the neuronal SNARE complex into the membrane (2009)

A. Stein ; G. Weber ; M. C. Wahl ; [et al.]

Nature Publishing Group (NPG)

In: Nature. 460(7254): 525-8. doi: 10.1038/nature08156.

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Publication Date: 2009-07-03

Description: Neurotransmission relies on synaptic vesicles fusing with the membrane of nerve cells to release their neurotransmitter content into the synaptic cleft, a process requiring the assembly of several members of the SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) family. SNAREs represent an evolutionarily conserved protein family that mediates membrane fusion in the secretory and endocytic pathways of eukaryotic cells. On membrane contact, these proteins assemble in trans between the membranes as a bundle of four alpha-helices, with the energy released during assembly being thought to drive fusion. However, it is unclear how the energy is transferred to the membranes and whether assembly is conformationally linked to fusion. Here, we report the X-ray structure of the neuronal SNARE complex, consisting of rat syntaxin 1A, SNAP-25 and synaptobrevin 2, with the carboxy-terminal linkers and transmembrane regions at 3.4 A resolution. The structure shows that assembly proceeds beyond the already known core SNARE complex, resulting in a continuous helical bundle that is further stabilized by side-chain interactions in the linker region. Our results suggest that the final phase of SNARE assembly is directly coupled to membrane merger.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3108252/" 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/PMC3108252/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Stein, Alexander -- Weber, Gert -- Wahl, Markus C -- Jahn, Reinhard -- P01 GM072694/GM/NIGMS NIH HHS/ -- P01 GM072694-01/GM/NIGMS NIH HHS/ -- England -- Nature. 2009 Jul 23;460(7254):525-8. doi: 10.1038/nature08156. Epub 2009 Jul 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Neurobiology, Max Planck Institute for Biophysical Chemistry, 37077 Gottingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19571812" target="_blank"〉PubMed〈/a〉

Keywords: Animals ; Crystallography, X-Ray ; Membrane Proteins/*chemistry ; Mice ; *Models, Molecular ; Neurons/*metabolism ; Protein Stability ; Protein Structure, Quaternary ; Rats ; SNARE Proteins/*chemistry/*metabolism ; Synapses/metabolism ; Syntaxin 1/chemistry ; Transition Temperature ; Vesicle-Associated Membrane Protein 2/chemistry

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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Binding of the human Prp31 Nop domain to a composite RNA-protein platform in U4 snRNP (2007)

S. Liu ; P. Li ; O. Dybkov ; [et al.]

American Association for the Advancement of Science (AAAS)

In: Science. 316(5821): 115-20. doi: 10.1126/science.1137924.

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Publication Date: 2007-04-07

Description: Although highly homologous, the spliceosomal hPrp31 and the nucleolar Nop56 and Nop58 (Nop56/58) proteins recognize different ribonucleoprotein (RNP) particles. hPrp31 interacts with complexes containing the 15.5K protein and U4 or U4atac small nuclear RNA (snRNA), whereas Nop56/58 associate with 15.5K-box C/D small nucleolar RNA complexes. We present structural and biochemical analyses of hPrp31-15.5K-U4 snRNA complexes that show how the conserved Nop domain in hPrp31 maintains high RNP binding selectivity despite relaxed RNA sequence requirements. The Nop domain is a genuine RNP binding module, exhibiting RNA and protein binding surfaces. Yeast two-hybrid analyses suggest a link between retinitis pigmentosa and an aberrant hPrp31-hPrp6 interaction that blocks U4/U6-U5 tri-snRNP formation.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Liu, Sunbin -- Li, Ping -- Dybkov, Olexandr -- Nottrott, Stephanie -- Hartmuth, Klaus -- Luhrmann, Reinhard -- Carlomagno, Teresa -- Wahl, Markus C -- New York, N.Y. -- Science. 2007 Apr 6;316(5821):115-20.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Abteilung Zellulare Biochemie, Max-Planck-Institut fur Biophysikalische Chemie, Am Fassberg 11, D-37077 Gottingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/17412961" target="_blank"〉PubMed〈/a〉

Keywords: Amino Acid Motifs ; Amino Acid Sequence ; Amino Acid Substitution ; Carrier Proteins/chemistry/metabolism ; Eye Proteins/*chemistry/*metabolism ; Humans ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Mutation ; Nucleic Acid Conformation ; Protein Binding ; Protein Conformation ; Protein Structure, Secondary ; Protein Structure, Tertiary ; RNA, Small Nuclear/*chemistry/*metabolism ; RNA-Binding Proteins ; Retinitis Pigmentosa/genetics ; Ribonucleoprotein, U4-U6 Small Nuclear/*chemistry/*metabolism ; Transcription Factors

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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A NusE:NusG complex links transcription and translation (2010)

B. M. Burmann ; K. Schweimer ; X. Luo ; [et al.]

American Association for the Advancement of Science (AAAS)

In: Science. 328(5977): 501-4. doi: 10.1126/science.1184953.

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Publication Date: 2010-04-24

Description: Bacterial NusG is a highly conserved transcription factor that is required for most Rho activity in vivo. We show by nuclear magnetic resonance spectroscopy that Escherichia coli NusG carboxyl-terminal domain forms a complex alternatively with Rho or with transcription factor NusE, a protein identical to 30S ribosomal protein S10. Because NusG amino-terminal domain contacts RNA polymerase and the NusG carboxy-terminal domain interaction site of NusE is accessible in the ribosomal 30S subunit, NusG may act as a link between transcription and translation. Uncoupling of transcription and translation at the ends of bacterial operons enables transcription termination by Rho factor, and competition between ribosomal NusE and Rho for NusG helps to explain why Rho cannot terminate translated transcripts.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Burmann, Bjorn M -- Schweimer, Kristian -- Luo, Xiao -- Wahl, Markus C -- Stitt, Barbara L -- Gottesman, Max E -- Rosch, Paul -- GM037219/GM/NIGMS NIH HHS/ -- New York, N.Y. -- Science. 2010 Apr 23;328(5977):501-4. doi: 10.1126/science.1184953.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Lehrstuhl Biopolymere und Forschungszentrum fur Bio-Makromolekule, Universitat Bayreuth, Universitatsstrasse 30, 95447 Bayreuth, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/20413501" target="_blank"〉PubMed〈/a〉

Keywords: Amino Acid Sequence ; Binding Sites ; Binding, Competitive ; DNA-Directed RNA Polymerases/metabolism ; Escherichia coli/genetics/*metabolism ; Escherichia coli Proteins/biosynthesis/chemistry/*genetics/metabolism ; Hydrophobic and Hydrophilic Interactions ; Models, Molecular ; Molecular Sequence Data ; Nuclear Magnetic Resonance, Biomolecular ; Operon ; Peptide Elongation Factors/chemistry/*metabolism ; Protein Binding ; *Protein Biosynthesis ; Protein Conformation ; Protein Interaction Domains and Motifs ; Protein Structure, Tertiary ; Ribosomal Proteins/chemistry/*metabolism ; Ribosome Subunits, Small, Bacterial/metabolism ; Transcription Factors/chemistry/*metabolism ; *Transcription, Genetic

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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Inhibition of RNA helicase Brr2 by the C-terminal tail of the spliceosomal protein Prp8 (2013)

S. Mozaffari-Jovin ; T. Wandersleben ; K. F. Santos ; [et al.]

American Association for the Advancement of Science (AAAS)

In: Science. 341(6141): 80-4. doi: 10.1126/science.1237515.

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Publication Date: 2013-05-25

Description: The Ski2-like RNA helicase Brr2 is a core component of the spliceosome that must be tightly regulated to ensure correct timing of spliceosome activation. Little is known about mechanisms of regulation of Ski2-like helicases by protein cofactors. Here we show by crystal structure and biochemical analyses that the Prp8 protein, a major regulator of the spliceosome, can insert its C-terminal tail into Brr2's RNA-binding tunnel, thereby intermittently blocking Brr2's RNA-binding, adenosine triphosphatase, and U4/U6 unwinding activities. Inefficient Brr2 repression is the only recognizable phenotype associated with certain retinitis pigmentosa-linked Prp8 mutations that map to its C-terminal tail. Our data show how a Ski2-like RNA helicase can be reversibly inhibited by a protein cofactor that directly competes with RNA substrate binding.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Mozaffari-Jovin, Sina -- Wandersleben, Traudy -- Santos, Karine F -- Will, Cindy L -- Luhrmann, Reinhard -- Wahl, Markus C -- New York, N.Y. -- Science. 2013 Jul 5;341(6141):80-4. doi: 10.1126/science.1237515. Epub 2013 May 23.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Cellular Biochemistry, Max Planck Institute for Biophysical Chemistry, Gottingen, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23704370" target="_blank"〉PubMed〈/a〉

Keywords: Amino Acid Motifs ; Amino Acid Sequence ; *Binding, Competitive ; Carrier Proteins/genetics/*metabolism ; Humans ; Molecular Sequence Data ; Mutation ; Protein Structure, Tertiary ; RNA/*metabolism ; RNA Helicases/metabolism ; RNA-Binding Proteins ; Ribonucleoprotein, U4-U6 Small Nuclear/metabolism ; Ribonucleoprotein, U5 Small Nuclear/metabolism ; Ribonucleoproteins, Small Nuclear/*antagonists & inhibitors/chemistry/*metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Spliceosomes/*metabolism ; Substrate Specificity

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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6

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Structure of the Purine–Pyrimidine Alternating RNA Double Helix, r(GUAUAUA)d(C), with a 3'-Terminal Deoxy Residue (1996)

Wahl, M. C. ; Ban, C. ; Sekharudu, C. ; [et al.]

Copenhagen : International Union of Crystallography (IUCr)

Acta crystallographica 52 (1996), S. 655-667

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ISSN: 1399-0047

Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001

Topics: Chemistry and Pharmacology , Geosciences , Physics

Notes: The crystal structure of the purine-pyrimidine alternating octameric RNA helix, r(GUAUAUA)d(C), carrying a 3′-terminal deoxycytidine residue, has been determined at 2.2 Å resolution. The molecule crystallizes in the rhombohedral space group R3 (hexagonal cell constants: a = b = 43.07,c = 59.36 Å;α = β = 90,γ = 120°)with one duplex in an asymmetric unit. The structure was solved by molecular replacement and refined with 83 and 2/3 solvent molecules and 2/3 sodium ions to a final R factor of 15.6% using 1775 reflections (86%). The duplexes are approximately linear, their global helix axes are inclined by 10° with respect to the 32-screw axes, and they are stacked on top of each other in a head-to-tail fashion. The twist between the junction base pairs of the stacked duplexes is negligible resulting in a discontinuity of the helix backbones and grooves. The sodium ions on the threefold axis play a significant role in the organization of the packing network. The helical parameters, particularly the twist and the roll, of this alternating sequence are in accord with Calladine's rules. Almost all the 2′-hydroxyl groups are involved in specific hydrogen-bonding interactions, either directly to the sugar ring oxygens O4′ on the 3′ side, or, through water bridges, to the sugars, phosphates, or bases. This hydrogen bonding of the 2′-hydroxyl groups restrains the conformation of the sugar-phosphate backbone and the glycosidic torsion angles of this RNA fragment. The lack of intermolecular packing contacts in the grooves provides a clear picture of the groove solvation.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1107/S0907444996000248

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Electronic Resource

RNA – Synthesis, Purification and Crystallization (1996)

Wahl, M. C. ; Ramakrishnan, B. ; Ban, C. ; [et al.]

Copenhagen : International Union of Crystallography (IUCr)

Acta crystallographica 52 (1996), S. 668-675

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ISSN: 1399-0047

Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001

Topics: Chemistry and Pharmacology , Geosciences , Physics

Notes: Protocols for the routine chemical synthesis and purification of milligram quantities of RNA and DNA-RNA chimeras meeting the demands of X-ray crystallography are described. An efficient screening protocol to test the crystallizability of the molecules and the optimization of the crystallization conditions are presented, so as to allow reproduction by others. Essentially the same crystallization conditions as for DNA oligomers can be employed for RNA crystallization. Specific examples involving alternating octamers, G/C-rich decamers, sequences with overhangs, and drug complexes of chimeras are discussed. Success of the methods is attested by the crystals obtained which diffract to high resolution.

Type of Medium: Electronic Resource

URL: http://dx.doi.org/10.1107/S0907444996002788

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