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Rupe De Wachte - One of the best experts on this subject based on the ideXlab platform.
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database on the structure of large Ribosomal Subunit rna
Nucleic Acids Research, 1994Co-Authors: P De Rijk, Yves Van De Pee, Rupe De WachteAbstract:The latest release of the large Ribosomal Subunit RNA database contains 429 sequences. All these sequences are aligned, and incorporate secondary structure information. The rRNA WWW Server at URL http://rrna.uia.ac.be/ provides researchers with an easily accessible resource to obtain the data in this database in a number of computer-readable formats. A new query interface has been added to the server. If necessary, the data can also be obtained by anonymous ftp from the same site.
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compilation of small Ribosomal Subunit rna structures
Nucleic Acids Research, 1993Co-Authors: Jeanmarc Neefs, P De Rijk, Yves Van De Pee, Sabine Chapelle, Rupe De WachteAbstract:Abstract The database on small Ribosomal Subunit RNA structure contained 1804 nucleotide sequences on April 23, 1993. This number comprises 365 eukaryotic, 65 archaeal, 1260 bacterial, 30 plastidial, and 84 mitochondrial sequences. These are stored in the form of an alignment in order to facilitate the use of the database as input for comparative studies on higher-order structure and for reconstruction of phylogenetic trees. The elements of the postulated secondary structure for each molecule are indicated by special symbols. The database is available on-line directly from the authors by ftp and can also be obtained from the EMBL nucleotide sequence library by electronic mail, ftp, and on CD ROM disk.
P De Rijk - One of the best experts on this subject based on the ideXlab platform.
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database on the structure of large Ribosomal Subunit rna
Nucleic Acids Research, 1994Co-Authors: P De Rijk, Yves Van De Pee, Rupe De WachteAbstract:The latest release of the large Ribosomal Subunit RNA database contains 429 sequences. All these sequences are aligned, and incorporate secondary structure information. The rRNA WWW Server at URL http://rrna.uia.ac.be/ provides researchers with an easily accessible resource to obtain the data in this database in a number of computer-readable formats. A new query interface has been added to the server. If necessary, the data can also be obtained by anonymous ftp from the same site.
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Database on the structure of large Ribosomal Subunit RNA.
Nucleic acids research, 1994Co-Authors: P De Rijk, Y Van De Peer, S Chapelle, R De WachterAbstract:A database on large Ribosomal Subunit RNA is made available. It contains 258 sequences. It provides sequence, alignment and secondary structure information in computer-readable formats. Files can be obtained using ftp.
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compilation of small Ribosomal Subunit rna structures
Nucleic Acids Research, 1993Co-Authors: Jeanmarc Neefs, P De Rijk, Yves Van De Pee, Sabine Chapelle, Rupe De WachteAbstract:Abstract The database on small Ribosomal Subunit RNA structure contained 1804 nucleotide sequences on April 23, 1993. This number comprises 365 eukaryotic, 65 archaeal, 1260 bacterial, 30 plastidial, and 84 mitochondrial sequences. These are stored in the form of an alignment in order to facilitate the use of the database as input for comparative studies on higher-order structure and for reconstruction of phylogenetic trees. The elements of the postulated secondary structure for each molecule are indicated by special symbols. The database is available on-line directly from the authors by ftp and can also be obtained from the EMBL nucleotide sequence library by electronic mail, ftp, and on CD ROM disk.
Galina G. Karpova - One of the best experts on this subject based on the ideXlab platform.
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a region in the c terminal domain of Ribosomal protein sa required for binding of sa to the human 40s Ribosomal Subunit
Biochimie, 2011Co-Authors: Alexey A. Malygin, Elena S. Babaylova, Valery B. Loktev, Galina G. KarpovaAbstract:The human Ribosomal protein SA, known also as a precursor of the cell-surface laminin receptor, LAMR, is a protein of the 40S Ribosomal Subunit. It is homologous to eubacterial Ribosomal protein S2p, but has a eukaryote-specific C-terminal domain (CTD) that is responsible in LAMR for the binding of laminin as well as prions and several viruses. Using serial deletions in the SA CTD, we showed that region between amino acids 236–262 is required for binding of the protein to 40S Ribosomal Subunits. All SA mutants containing this region protected nucleotides in hairpin 40 (which is not bound to any protein in the eubacterial 30S Ribosomal Subunit) of the 18S rRNA from hydroxyl radical attack. Comparison of our data with the cryo-EM models of the mammalian 40S Ribosomal Subunit allowed us to locate the SA CTD in the spatial structure of the 40S Subunit.
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Binding of the IRES of hepatitis C virus RNA to the 40S Ribosomal Subunit: role of protein p40
Molekuliarnaia biologiia, 2009Co-Authors: Alexey A. Malygin, E I Bondarenko, Valery B. Loktev, Z. V. Bochkaeva, O A Kosinova, I N Shatskiĭ, Galina G. KarpovaAbstract:Ribosomal protein p40 is a structural component of the 40S Ribosomal Subunit, which is partially homologuos to prokaryotic Ribosomal protein S2 and has a long eukaryote-specific C-terminal region. In the present work, we have studied the binding of the Internal Ribosome Entry Site (IRES) of the hepatitis C virus (HCV) RNA to the 40S Ribosomal Subunit either deficient on protein p40, or saturated with the recombinant p40, or pre-bound to monoclonal antibodies (MAB) 4F6 against p40. It was shown that the apparent association constant of HCV IRES binding to 40S Subunits directly depends on p40 content in the Subunits. Binding of MAB 4F6 against p40 to 40S Subunits prevented the HCV IRES binding by the Subunits and blocked translation of the IRES-containing RNA in cell-free translation system. The data obtained point to the involvement of the Ribosomal protein p40 in the binding of the HCV IRES by ribosomes and therefore in initiation of translation of RNA of this virus.
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proteins surrounding hairpin iiie of the hepatitis c virus internal ribosome entry site on the human 40s Ribosomal Subunit
Nucleic Acids Research, 2006Co-Authors: E S Laletina, Anton V. Ivanov, Dmitri M Graifer, Ivan N. Shatsky, Alexey A. Malygin, Galina G. KarpovaAbstract:Binding of the internal ribosome entry site (IRES) of the hepatitis C virus (HCV) RNA to the eIF-free 40S Ribosomal Subunit is the first step of initiation of translation of the viral RNA. Hairpins IIId and IIIe comprising 253–302 nt of the IRES are known to be essential for binding to the 40S Subunit. Here we have examined the molecular environment of the HCV IRES in its binary complex with the human 40S Ribosomal Subunit. For this purpose, two RNA derivatives were used that bore a photoactivatable perfluorophenyl azide cross-linker. In one derivative the cross-linker was at the nucleotide A296 in hairpin IIIe, and in the other at G87 in domain II. Site-specific introduction of the cross-linker was performed using alkylating derivatives of oligodeoxyribonucleotides complementary to the target RNA sequences. No cross-links with the rRNA were detected with either RNA derivative. The RNA with the photoactivatable group at A296 cross-linked to proteins identified as S5 and S16 (major) and p40 and S3a (minor), while no cross-links with proteins were detected with RNA modified at G87. The results obtained indicate that hairpin IIIe is located on the solvent side of the 40S Subunit head on a site opposite the beak.
Patrick Linder - One of the best experts on this subject based on the ideXlab platform.
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Dbp9p, a putative ATP-dependent RNA helicase involved in 60S-Ribosomal-Subunit biogenesis, functionally interacts with Dbp6p.
RNA, 2001Co-Authors: Marie-claire Daugeron, Dieter Kressler, Patrick LinderAbstract:Ribosome synthesis is a highly complex process and constitutes a major cellular activity. The biogenesis of this ribonucleoprotein assembly requires a multitude of protein trans-acting factors including several putative ATPdependent RNA helicases of the DEAD-box and related protein families. Here we show that the previously uncharacterized Saccharomyces cerevisiae open reading frame YLR276C, hereafter named DBP9 (DEAD-box protein 9), encodes an essential nucleolar protein involved in 60S-Ribosomal-Subunit biogenesis. Genetic depletion of Dbp9p results in a deficit in 60S Ribosomal Subunits and the appearance of half-mer polysomes. This terminal phenotype is likely due to the instability of early pre-Ribosomal particles, as evidenced by the low steady-state levels and the decreased synthesis of the 27S precursors to mature 25S and 5.8S rRNAs. In agreement with a role of Dbp9p in 60S Subunit synthesis, we find that increased Dbp9p dosage efficiently suppresses certain dbp6 alleles and that dbp6/ dbp9 double mutants show synthetic lethality. Furthermore, Dbp6p and Dbp9p weakly interact in a yeast two-hybrid assay. Altogether, our findings indicate an intimate functional interaction between Dbp6p and Dbp9p during the process of 60S-Ribosomal-Subunit assembly.
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Dbp7p, a putative ATP-dependent RNA helicase from Saccharomyces cerevisiae, is required for 60S Ribosomal Subunit assembly.
RNA, 1998Co-Authors: Marie-claire Daugeron, Patrick LinderAbstract:Putative ATP-dependent RNA helicases are ubiquitous, highly conserved proteins that are found in most organisms and they are implicated in all aspects of cellular RNA metabolism. Here we present the functional characterization of the Dbp7 protein, a putative ATP-dependent RNA helicase of the DEAD-box protein family from Saccharomyces cerevisiae. The complete deletion of the DBP7 ORF causes a severe slow-growth phenotype. In addition, the absence of Dbp7p results in a reduced amount of 60S Ribosomal Subunits and an accumulation of halfmer polysomes. Subsequent analysis of pre-rRNA processing indicates that this 60S Ribosomal Subunit deficit is due to a strong decrease in the production of 27S and 7S precursor rRNAs, which leads to reduced levels of the mature 25S and 5.8S rRNAs. Noticeably, the overall decrease of the 27S pre-rRNA species is neither associated with the accumulation of preceding precursors nor with the emergence of abnormal processing intermediates, suggesting that these 27S pre-rRNA species are degraded rapidly in the absence of Dbp7p. Finally, an HA epitope-tagged Dbp7 protein is localized in the nucleolus. We propose that Dbp7p is involved in the assembly of the pre-Ribosomal particle during the biogenesis of the 60S Ribosomal Subunit.
Thomas A Steitz - One of the best experts on this subject based on the ideXlab platform.
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Structures of Triacetyloleandomycin and Mycalamide A Bind to the Large Ribosomal Subunit of Haloarcula marismortui
Antimicrobial Agents and Chemotherapy, 2009Co-Authors: G. Gurel, Thomas A Steitz, Gregor Blaha, Peter B. MooreAbstract:Structures have been obtained for the complexes that triacetyloleandomycin and mycalamide A form with the large Ribosomal Subunit of Haloarcula marismortui. Triacetyloleandomycin binds in the nascent peptide tunnel and inhibits the activity of ribosomes by blocking the growth of the nascent peptide chain. Mycalamide A binds to the E site and inhibits protein synthesis by occupying the space normally occupied by the CCA end of E-site-bound tRNAs.
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the structures of four macrolide antibiotics bound to the large Ribosomal Subunit
Molecular Cell, 2002Co-Authors: J L Hansen, Peter B. Moore, Poul Nissen, Thomas A Steitz, Joseph A IppolitoAbstract:Abstract Crystal structures of the Haloarcula marismortui large Ribosomal Subunit complexed with the 16-membered macrolide antibiotics carbomycin A, spiramycin, and tylosin and a 15-membered macrolide, azithromycin, show that they bind in the polypeptide exit tunnel adjacent to the peptidyl transferase center. Their location suggests that they inhibit protein synthesis by blocking the egress of nascent polypeptides. The saccharide branch attached to C5 of the lactone rings extends toward the peptidyl transferase center, and the isobutyrate extension of the carbomycin A disaccharide overlaps the A-site. Unexpectedly, a reversible covalent bond forms between the ethylaldehyde substituent at the C6 position of the 16-membered macrolides and the N6 of A2103 (A2062, E. coli ). Mutations in 23S rRNA that result in clinical resistance render the binding site less complementary to macrolides.
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rna tertiary interactions in the large Ribosomal Subunit the a minor motif
Proceedings of the National Academy of Sciences of the United States of America, 2001Co-Authors: Poul Nisse, Joseph A Ippolito, Nenad A, Pete Moore, Thomas A SteitzAbstract:Analysis of the 2.4-A resolution crystal structure of the large Ribosomal Subunit from Haloarcula marismortui reveals the existence of an abundant and ubiquitous structural motif that stabilizes RNA tertiary and quaternary structures. This motif is termed the A-minor motif, because it involves the insertion of the smooth, minor groove edges of adenines into the minor groove of neighboring helices, preferentially at C-G base pairs, where they form hydrogen bonds with one or both of the 2' OHs of those pairs. A-minor motifs stabilize contacts between RNA helices, interactions between loops and helices, and the conformations of junctions and tight turns. The interactions between the 3' terminal adenine of tRNAs bound in either the A site or the P site with 23S rRNA are examples of functionally significant A-minor interactions. The A-minor motif is by far the most abundant tertiary structure interaction in the large Ribosomal Subunit; 186 adenines in 23S and 5S rRNA participate, 68 of which are conserved. It may prove to be the universally most important long-range interaction in large RNA structures.
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the complete atomic structure of the large Ribosomal Subunit at 2 4 a resolution
Science, 2000Co-Authors: Nenad Ban, Peter B. Moore, Poul Nissen, J L Hansen, Thomas A SteitzAbstract:The large Ribosomal Subunit catalyzes peptide bond formation and binds initiation, termination, and elongation factors. We have determined the crystal structure of the large Ribosomal Subunit from Haloarcula marismortui at 2.4 angstrom resolution, and it includes 2833 of the Subunit's 3045 nucleotides and 27 of its 31 proteins. The domains of its RNAs all have irregular shapes and fit together in the ribosome like the pieces of a three-dimensional jigsaw puzzle to form a large, monolithic structure. Proteins are abundant everywhere on its surface except in the active site where peptide bond formation occurs and where it contacts the small Subunit. Most of the proteins stabilize the structure by interacting with several RNA domains, often using idiosyncratically folded extensions that reach into the Subunit's interior.