当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > Identification of a GUAAY Pentaloop Sequence Involved in a Novel RNA Loop-Helix Interaction.

Identification of a GUAAY Pentaloop Sequence Involved in a Novel RNA Loop-Helix Interaction.

Abstract：

:Large RNAs often utilize GNRA tetraloops as structural elements to stabilize the overall tertiary fold. These tetraloop-receptor (TR) interactions have a conserved geometry in which the tetraloop docks into the receptor at an angle of ~15° from the helix containing the receptor. Here, we show that the conserved GUAAY pentaloop found in domain III of group IIB1 introns participates in a novel class of RNA tertiary interaction with a geometry and mode of binding that are significantly different from that found in GNRA TR interactions. This pentaloop is highly conserved within the IIB1 class and interacts with the minor groove of the catalytic domain V. The base planes of the loop and receptor nucleotides are not coplanar and greatly deviate from standard A-minor motifs. The helical axis of the GUAAY stem loop diverges ~70° from the angle of insertion found in a typical GNRA TR interaction. Therefore, the loop architecture and insertion orientation are distinctive, with in vitro splicing data indicating that a GNRA tetraloop is incompatible at this position. The GUAAY pentaloop-receptor motif is also found in the structure of the eukaryotic thiamine pyrophosphate riboswitch in the context of a hexanucleotide loop sequence. We therefore propose, based on phylogenetic, structural, and biochemical data, that the GUAAY pentaloop-receptor interaction represents a novel structural motif that is present in multiple structured RNAs.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Chan RT,Keating KS,Go MC,Toor N

doi

10.1016/j.jmb.2016.10.015

subject

Has Abstract

pub_date

2016-12-04 00:00:00

pages

4882-4889

issue

24 Pt B

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(16)30430-2

journal_volume

428

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • The P-glycoprotein gene family of Caenorhabditis elegans. Cloning and characterization of genomic and complementary DNA sequences.

    abstract：:P-glycoproteins, encoded by families of evolutionarily conserved genes, can confer a multidrug-resistant phenotype to mammalian tumor cells. To obtain more information on their functions in normal cells we have cloned genomic and complementary DNA sequences of four P-glycoprotein gene homologs of the genetically well-...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(92)90855-e

    authors： Lincke CR,The I,van Groenigen M,Borst P

    更新日期：1992-11-20 00:00:00

  • Structure and mechanism of the magnesium-independent aromatic prenyltransferase CloQ from the clorobiocin biosynthetic pathway.

    abstract：:CloQ is an aromatic prenyltransferase from the clorobiocin biosynthetic pathway of Streptomyces roseochromogenes var. oscitans. It is involved in the synthesis of the prenylated hydroxybenzoate moiety of the antibiotic, specifically catalyzing the attachment of a dimethylallyl moiety to 4-hydroxyphenylpyruvate. Herein...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2010.09.067

    authors： Metzger U,Keller S,Stevenson CE,Heide L,Lawson DM

    更新日期：2010-12-10 00:00:00

  • New features of the ribosome and ribosomal inhibitors: non-enzymatic recycling, misreading and back-translocation.

    abstract：:We describe the optimization of a poly(Phe) synthesis system, the conditions of which have been applied for efficient translation of heteropolymeric mRNAs. Here we identify two parameters that are essential to obtain translation at efficiency and accuracy levels equivalent to those in vivo, viz., the fine-tuning of th...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.04.060

    authors： Szaflarski W,Vesper O,Teraoka Y,Plitta B,Wilson DN,Nierhaus KH

    更新日期：2008-06-27 00:00:00

  • Cysteine residue periodicity is a conserved structural feature of variable surface proteins from Paramecium tetraurelia.

    abstract：:The DNA sequences of the entire coding regions of the A and C type variable surface protein genes from Paramecium tetraurelia, stock 51 have been determined. The 8151 nucleotide open reading frame of the A gene contains several tandem repeats of 210 nucleotides within the central portion of the molecule as well as a p...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90573-o

    authors： Nielsen E,You Y,Forney J

    更新日期：1991-12-20 00:00:00

  • Multiple sequence threading: an analysis of alignment quality and stability.

    abstract：:Methods that compare a protein sequence directly to a structure can be divided into those that construct a molecular model (threading methods) and those that perform a sequence alignment with the structure encoded as a sequence of structural states (one-dimensional/three-dimensional (1D/3D) matching). The former take ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1997.1008

    authors： Taylor WR

    更新日期：1997-06-27 00:00:00

  • Islet amyloid polypeptide inserts into phospholipid monolayers as monomer.

    abstract：:Amyloid deposits in the pancreatic islets of Langerhans are thought to be a main factor responsible for death of the insulin-producing islet beta-cells in type 2 diabetes. It is hypothesized that beta-cell death is related to interaction of the 37 amino acid residue human islet amyloid polypeptide (hIAPP), the major c...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.12.020

    authors： Engel MF,Yigittop H,Elgersma RC,Rijkers DT,Liskamp RM,de Kruijff B,Höppener JW,Antoinette Killian J

    更新日期：2006-02-24 00:00:00

  • Structural and functional analysis of a human 7 S K RNA gene.

    abstract：:Using purified RNA from HeLa cells, we have synthesized and cloned a cDNA encoding an almost entire 7 S K RNA. This cDNA probe was used to isolate 7 S K RNA gene sequences from a human genomic library by high-stringency colony hybridization. In order to differentiate between functional genes and related sequences, we ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(87)90325-1

    authors： Krüger W,Benecke BJ

    更新日期：1987-05-05 00:00:00

  • A TOPRIM domain in the crystal structure of the catalytic core of Escherichia coli primase confirms a structural link to DNA topoisomerases.

    abstract：:Primases synthesize short RNA strands on single-stranded DNA templates, thereby generating the hybrid duplexes required for the initiation of synthesis by DNA polymerases. We present the crystal structure of the catalytic unit of a primase enzyme, that of a approximately 320 residue fragment of Escherichia coli primas...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.3844

    authors： Podobnik M,McInerney P,O'Donnell M,Kuriyan J

    更新日期：2000-07-07 00:00:00

  • Decomposition of the free energy of a system in terms of specific interactions. Implications for theoretical and experimental studies.

    abstract：:Recently, a number of methods have been proposed that are designed to extract contributions to the change in free energy associated with a given perturbation or mutation of a protein originating from specific residue-residue or atom-atom interactions, both based on theoretical calculations and on experimental data. We...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1430

    authors： Mark AE,van Gunsteren WF

    更新日期：1994-07-08 00:00:00

  • Characterization of a conserved alpha-helical, coiled-coil motif at the C-terminal domain of the ATP-dependent FtsH (HflB) protease of Escherichia coli.

    abstract：:FtsH (HflB) is an ATP-dependent protease found in prokaryotic cells, mitochondria and chloroplasts. Here, we have identified, in the carboxy-terminal region of FtsH (HfIB), a short alpha helix predicted of forming a coiled-coil, leucine zipper, structure. This region appears to be structurally conserved. The presence ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.3767

    authors： Shotland Y,Teff D,Koby S,Kobiler O,Oppenheim AB

    更新日期：2000-06-16 00:00:00

  • Transfer of flexibility between ankyrin repeats in IkappaB* upon formation of the NF-kappaB complex.

    abstract：:The mechanism of inhibition of the transcriptional activator nuclear factor kappaB (NF-kappaB) by the inhibitor IkappaB* is central to the understanding of the control of transcriptional activity via this widely employed pathway. Previous studies suggested that IkappaB* , a modular protein with an NF-kappaB binding do...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.05.048

    authors： Sue SC,Cervantes C,Komives EA,Dyson HJ

    更新日期：2008-07-25 00:00:00

  • Tandemization endows bovine pancreatic ribonuclease with cytotoxic activity.

    abstract：:Due to their ability to degrade RNA, selected members of the bovine pancreatic ribonuclease A (RNase A) superfamily are potent cytotoxins. These cytotoxic ribonucleases enter the cytosol of target cells, where they degrade cellular RNA and cause cell death. The cytotoxic activity of most RNases, however, is abolished ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2006.03.007

    authors： Leich F,Köditz J,Ulbrich-Hofman R,Arnold U

    更新日期：2006-05-19 00:00:00

  • Molecular model of an alpha-helical prion protein dimer and its monomeric subunits as derived from chemical cross-linking and molecular modeling calculations.

    abstract：:Prions are the agents of a series of lethal neurodegenerative diseases. They are composed largely, if not entirely, of the host-encoded prion protein (PrP), which can exist in the cellular isoform PrP(C) and the pathological isoform PrP(Sc). The conformational change of the alpha-helical PrP(C) into beta-sheet-rich Pr...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.11.035

    authors： Kaimann T,Metzger S,Kuhlmann K,Brandt B,Birkmann E,Höltje HD,Riesner D

    更新日期：2008-02-15 00:00:00

  • Structure of alpha-chymotrypsin refined at 1.68 A resolution.

    abstract：:Diffraction data for alpha-chymotrypsin crystals at -10 degrees C were measured at 1.68 A resolution and refined by restrained structure-factor least-squares refinement. The two independent chymotrypsin molecules in the crystallographic asymmetric unit were refined independently. The overall structure of alpha-chymotr...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(85)90314-6

    authors： Tsukada H,Blow DM

    更新日期：1985-08-20 00:00:00

  • Effect of cytosine methylation on DNA-DNA recognition at CpG steps.

    abstract：:Although DNA methylation is a fundamental mechanism for repressing genetic activity, the influence of methyl groups on DNA conformation is found to be small. In this study, the role of cytosine methylation is analysed in the context of DNA condensation by examining its influence on DNA-DNA recognition processes. Previ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1997.1137

    authors： Mayer-Jung C,Moras D,Timsit Y

    更新日期：1997-07-18 00:00:00

  • Coupling of protein assembly and DNA binding: biotin repressor dimerization precedes biotin operator binding.

    abstract：:The kinetics of coupling of protein dimerization and DNA binding have been investigated in the biotin repressor system. Two repressor monomers bind to the 40 base-pair biotin operator sequence. In previous analyses of equilibrium-binding data the weak dimerization of the repressor has justified using a model in which ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(02)01308-6

    authors： Streaker ED,Beckett D

    更新日期：2003-01-31 00:00:00

  • Regulation of a promoter that is utilized by minor forms of RNA polymerase holoenzyme in Bacillus subtilis.

    abstract：:The ctc gene of Bacillus subtilis is transcribed in vitro by the minor RNA polymerase holoenzyme forms, E sigma 37 and E sigma 32. To study the expression and regulation of ctc in vivo, we constructed operon and translational fusions of the ctc promoter region to the lacZ gene of Escherichia coli. Our results indicate...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(86)90449-3

    authors： Igo MM,Losick R

    更新日期：1986-10-20 00:00:00

  • Next-generation pathology--surveillance of tumor microecology.

    abstract：:A tumor is a heterogeneous population of cells that provides an environment in which every cell resides in a microenvironmental niche. Microscopic evaluation of tissue sections, based on histology and immunohistochemistry, has been a cornerstone in pathology for decades. However, the dawn of novel technologies to inve...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2015.02.017

    authors： Koos B,Kamali-Moghaddam M,David L,Sobrinho-Simões M,Dimberg A,Nilsson M,Wählby C,Söderberg O

    更新日期：2015-06-05 00:00:00

  • Congruence of in vivo and in vitro insertion patterns in hot E. coli gene targets of transposable element Mu: opposing roles of MuB in target capture and integration.

    abstract：:Phage Mu transposes promiscuously, employing protein MuB for target capture. MuB forms stable filaments on A/T-rich DNA, and a correlation between preferred MuB binding and Mu integration has been observed. We have investigated the relationship between MuB-binding and Mu insertion into hot and cold Mu targets within t...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.05.032

    authors： Ge J,Harshey RM

    更新日期：2008-07-18 00:00:00

  • X-ray structure analysis and crystallographic refinement of lumazine synthase from the hyperthermophile Aquifex aeolicus at 1.6 A resolution: determinants of thermostability revealed from structural comparisons.

    abstract：:An open reading frame optimized for expression of 6,7-dimethyl-8-ribityl-lumazine synthase of the hyperthermophilic bacterium Aquifex aeolicus in Escherichia coli was synthesized and expressed in a recombinant E. coli strain to a level of around 15 %. The recombinant protein was purified by heat-treatment and gel-filt...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2000.4435

    authors： Zhang X,Meining W,Fischer M,Bacher A,Ladenstein R

    更新日期：2001-03-09 00:00:00

  • A complex nucleoprotein structure involved in activation of transcription of two divergent Escherichia coli promoters.

    abstract：:Initiation of transcription at malEp and malKp, two divergent Escherichia coli promoters, depends on the presence of both CRP, a pleiotropic activator, and MalT, the maltose regulon activator. We carried out in vivo genetic and functional analysis of these promoters and characterized their interaction with MalT and CR...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(89)90218-0

    authors： Raibaud O,Vidal-Ingigliardi D,Richet E

    更新日期：1989-02-05 00:00:00

  • Molecular and functional characterization of a carbon starvation gene of Escherichia coli.

    abstract：:Escherichia coli induces the synthesis of at least 30 proteins at the onset of carbon starvation, two-thirds of which are positively regulated by the cyclic AMP (cAMP) and cAMP receptor protein (CRP) complex. Two of the cAMP-CRP-dependent genes mapped to 14 and 93 minutes of the chromosome and are designated cstA and ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90879-b

    authors： Schultz JE,Matin A

    更新日期：1991-03-05 00:00:00

  • Molecular interplay between RNA polymerase and two transcriptional regulators in promoter switch.

    abstract：:Transcription regulation relies in the molecular interplay between the RNA polymerase (RNAP) and regulatory factors. Phage phi29 promoters A2c, A2b and A3 are coordinately regulated by the transcriptional regulator protein p4 and the histone-like protein p6. This study shows that protein p4 binds simultaneously to fou...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2003.12.039

    authors： Camacho A,Salas M

    更新日期：2004-02-13 00:00:00

  • Translational activation in coliphage Qbeta: on a polycistronic messenger RNA, repression of one gene can activate translation of another.

    abstract：:We present evidence for translational activation of the Qbeta coliphage maturation cistron, mediated by the presence of Qbeta replicase. This activation does not require RNA replication, translation of a second gene, or any direct protein-RNA binding at the maturation gene initiation site. Our data support a model in ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1997.1194

    authors： Priano C,Arora R,Jayant L,Mills DR

    更新日期：1997-08-22 00:00:00

  • A thymine-like base analogue forms wobble pairs with adenine in a Z-DNA duplex.

    abstract：:The DNA hexamer d(CACGPG), in which dP is the ambivalent pyrimidine nucleoside analogue 2'-deoxy-beta-d-ribofuranosyl-(6H,8H-3, 4-dihydropyrimido[4,5-c][1,2]oxazin-7-one), crystallises as a left-handed Z-DNA duplex. X-ray analysis at 1.5 A shows that both P. A base-pairs are of the wobble type. This result appears inc...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2080

    authors： Schuerman GS,Van Meervelt L,Loakes D,Brown DM,Kong Thoo Lin P,Moore MH,Salisbury SA

    更新日期：1998-10-09 00:00:00

  • Cloning and sequence analysis of the Escherichia coli 4.5 S RNA gene.

    abstract：:The structure of the Escherichia coli gene coding for the metabolically stable 4.5 S RNA has been determined by cloning and DNA sequence analysis. Results from Southern hybridization assays carried out prior to cloning show the 4.5 S DNA to be limited to a single locus in the E. coli K12 genome. A 5.4 X 10(3) base DNA...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(84)90236-5

    authors： Hsu LM,Zagorski J,Fournier MJ

    更新日期：1984-09-25 00:00:00

  • Interdomain contact regions and angles between adjacent short consensus repeat domains.

    abstract：:The short consensus repeat domain (SCR, complement control protein module, sushi-domain) is a structural unit found in multiple adjacent copies in more than 40 human proteins. Each bead-like domain is composed of approximately 60 residues and the adjacent domains are connected in a head-to-tail fashion with linkers th...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.10.017

    authors： Lehtinen MJ,Meri S,Jokiranta TS

    更新日期：2004-12-10 00:00:00

  • Specific mode of interaction between components of model pulmonary surfactants using computer simulations.

    abstract：:Atomistic molecular dynamics simulations and structural bioinformatics tools enable the identification of the exact mode of interaction between model pulmonary surfactant components. Two nanosecond long simulations of the N-terminal region of human surfactant protein-B (SP-B(1-25)) in dipalmitoylphosphatidylcholine (D...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/s0022-2836(02)00774-x

    authors： Kaznessis YN,Kim S,Larson RG

    更新日期：2002-09-20 00:00:00

  • Snapshots of RecA protein involving movement of the C-domain and different conformations of the DNA-binding loops: crystallographic and comparative analysis of 11 structures of Mycobacterium smegmatis RecA.

    abstract：:Mycobacterium smegmatis RecA and its nucleotide complexes crystallize in three different, but closely related, forms characterized by specific ranges of unit cell dimensions. The six crystals reported here and five reported earlier, all grown under the same or very similar conditions, belong to these three forms, all ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.01.058

    authors： Krishna R,Prabu JR,Manjunath GP,Datta S,Chandra NR,Muniyappa K,Vijayan M

    更新日期：2007-04-06 00:00:00

  • X-ray crystal structure of the rotavirus inner capsid particle at 3.8 A resolution.

    abstract：:The rotavirus inner capsid particle, known as the "double-layered particle" (DLP), is the "payload" delivered into a cell in the process of viral infection. Its inner and outer protein layers, composed of viral protein (VP) 2 and VP6, respectively, package the 11 segments of the double-stranded RNA (dsRNA) of the vira...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2010.01.055

    authors： McClain B,Settembre E,Temple BR,Bellamy AR,Harrison SC

    更新日期：2010-03-26 00:00:00