Xenopus poly(A) binding protein: functional domains in RNA binding and protein-protein interaction.


:Subsets of the four RNA binding domains (RBD 1 to 4) in the Xenopus poly-adenylate binding protein (PABP) have distinct affinities and specificities for RNA. RBDs 1 plus 2 exhibit RNA affinity and selectivity equal to the wild-type (WT) protein. RBDs 3 plus 4 have distinct selectivity and about ten-fold reduced affinity for A23, and the isolated RBDs 2 or 3 or 4 exhibit about 100-fold reduced affinity for A23 in comparison to WT. For the full-length protein, independent RNA contacts have been mapped by UV crosslinking with RBDs 1/2 and RBDs 3/4. The carboxy-terminal, non-RBD portion of the protein does not contribute to RNA affinity or selectivity, but confers homodimerization activity on PABP. RBDs 3 and 4 cooperate with the C terminus to gain poly(A) organizing activity, i.e. the ability to form an RNP with multiple, regularly spaced copies of PABP on a poly(A) substrate.


J Mol Biol


Kühn U,Pieler T




Has Abstract


1996-02-16 00:00:00














  • Mechanism of codon recognition by transfer RNA and codon-induced tRNA association.

    abstract::The steps of UUC recognition by tRNAPhe were analysed by temperature-jump measurements. At ion concentrations close to physiological conditions we found three relaxation processes, which we assigned to (1) formation of codon-anticodon complexes, (2) a conformational change of the anticodon loop coupled with Mg2+ bindi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Labuda D,Striker G,Porschke D

    更新日期:1984-04-25 00:00:00

  • The contribution of surface residues to membrane binding and ligand transfer by the α-tocopherol transfer protein (α-TTP).

    abstract::Previous work has shown that the α-tocopherol transfer protein (α-TTP) can bind to vesicular or immobilized phospholipid membranes. Revealing the molecular mechanisms by which α-TTP associates with membranes is thought to be critical to understanding its function and role in the secretion of tocopherol from hepatocyte...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Zhang WX,Thakur V,Lomize A,Pogozheva I,Panagabko C,Cecchini M,Baptist M,Morley S,Manor D,Atkinson J

    更新日期:2011-01-28 00:00:00

  • Folding of the Tetrahymena ribozyme by polyamines: importance of counterion valence and size.

    abstract::Polyamines are abundant metabolites that directly influence gene expression. Although the role of polyamines in DNA condensation is well known, their role in RNA folding is less understood. Non-denaturing gel electrophoresis was used to monitor the equilibrium folding transitions of the Tetrahymena ribozyme in the pre...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Koculi E,Lee NK,Thirumalai D,Woodson SA

    更新日期:2004-07-30 00:00:00

  • The salt-dependence of a protein-ligand interaction: ion-protein binding energetics.

    abstract::Using the binding of a nucleotide inhibitor (guanosine-3'-monophosphate) to a ribonuclease (ribonuclease Sa) as a model system, we show that the salt-dependence of the interaction arises due to specific ion binding at the site of nucleotide binding. The presence of specific ion-protein binding is concluded from a comb...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Waldron TT,Schrift GL,Murphy KP

    更新日期:2005-02-25 00:00:00

  • Binding mode prediction for a flexible ligand in a flexible pocket using multi-conformation simulated annealing pseudo crystallographic refinement.

    abstract::We describe multi-conformation simulated annealing-pseudo-crystallographic refinement (MCSA-PCR), a technique developed for predicting the binding mode of a flexible ligand in a flexible binding pocket. To circumvent the local-minimum problem efficiently, this method performs multiple independent cycles of simulated a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Ota N,Agard DA

    更新日期:2001-11-30 00:00:00

  • Effects of Mg2+, K+, and H+ on an equilibrium between alternative conformations of an RNA pseudoknot.

    abstract::A complex pseudoknot structure surrounds the first ribosome initiation site in the Escherichia coli alpha mRNA and mediates its regulation by ribosomal protein S4. A 112 nt RNA fragment containing this pseudoknot exists in two conformations that are resolvable by gel electrophoresis below room temperature. Between 30 ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Gluick TC,Gerstner RB,Draper DE

    更新日期:1997-07-18 00:00:00

  • Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility.

    abstract::The worm-like chain model has often been employed to describe the average conformation of long, intrinsically straight polymer molecules, including DNA. The present study extends the applicability of the worm-like chain model to polymers containing bends or sections of different flexibility. Several cases have been ex...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Rivetti C,Walker C,Bustamante C

    更新日期:1998-07-03 00:00:00

  • Transition of chromatin from the "10 nm" lower order structure, to the "30 nm" higher order structure as followed by small angle X-ray scattering.

    abstract::Chromatin oligomers undergo a conformational change from a "10 nm" lower order structure at low concentration of salt to a "30 nm" higher order structure, with increasing NaCl or MgCl2 concentration. We have extended our previously reported hydrodynamic and light-scattering measurements of the folding of well-defined ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Greulich KO,Wachtel E,Ausio J,Seger D,Eisenberg H

    更新日期:1987-02-20 00:00:00

  • Induction and myofibrillar targeting of CARP, and suppression of the Nkx2.5 pathway in the MDM mouse with impaired titin-based signaling.

    abstract::Muscular dystrophy with myositis (mdm) is a recessive mouse mutation that is caused by a small deletion in the giant elastic muscle protein titin. Homozygous mdm/mdm mice develop a progressive muscular dystrophy, leading to death at approximately 2 months of age. We surveyed the transcriptomes of skeletal muscles from...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Witt CC,Ono Y,Puschmann E,McNabb M,Wu Y,Gotthardt M,Witt SH,Haak M,Labeit D,Gregorio CC,Sorimachi H,Granzier H,Labeit S

    更新日期:2004-02-06 00:00:00

  • Crystal structures of phosphotransferase system enzymes PtxB (IIB(Asc)) and PtxA (IIA(Asc)) from Streptococcus mutans.

    abstract::Streptococcus mutans is the primary etiological agent of dental caries in man and other mammalian organisms. This bacterium metabolizes carbohydrates actively and thrives under anaerobic conditions by fermenting l-ascorbate (Asc) via the sga operon, which includes SgaT, PtxB, and PtxA. These three proteins are members...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Lei J,Li LF,Su XD

    更新日期:2009-02-20 00:00:00

  • Isolation of human antibody repertoires with preservation of the natural heavy and light chain pairing.

    abstract::The humoral immune system in higher vertebrates is unique in its ability to generate highly diverse antibody responses against most pathogens as well as against certain malignancies. Several technologies have been developed to exploit this vast source of potentially therapeutic antibodies, including hybridoma technolo...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Meijer PJ,Andersen PS,Haahr Hansen M,Steinaa L,Jensen A,Lantto J,Oleksiewicz MB,Tengbjerg K,Poulsen TR,Coljee VW,Bregenholt S,Haurum JS,Nielsen LS

    更新日期:2006-05-05 00:00:00

  • Crystallographic structure of phosphofructokinase-2 from Escherichia coli in complex with two ATP molecules. Implications for substrate inhibition.

    abstract::Phosphofructokinase-1 and -2 (Pfk-1 and Pfk-2, respectively) from Escherichia coli belong to different homologous superfamilies. However, in spite of the lack of a common ancestor, they share the ability to catalyze the same reaction and are inhibited by the substrate MgATP. Pfk-2, an ATP-dependent 6-phosphofructokina...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Cabrera R,Ambrosio AL,Garratt RC,Guixé V,Babul J

    更新日期:2008-11-14 00:00:00

  • Crystallization and preliminary crystallographic data of the Fab fragment of an anti-phenylalanine hydroxylase monoclonal antibody.

    abstract::Two crystal habits, one rod shaped and the other square prismatic, of the Fab fragment of a monoclonal anti-phenylalanine hydroxylase antibody have been grown using the method of vapour phase diffusion against polyethylene glycol 6000. The square prisms diffract to better than 2.8 A, belong to the space group P1 and h...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Guddat LW,Cowan SW,Machin KJ,Isaacs NW,Cotton RG

    更新日期:1985-11-20 00:00:00

  • A crystallographic re-investigation into the structure of Streptomyces griseus proteinase A reveals an acyl-enzyme intermediate.

    abstract::A molecular dynamics (MD) simulation on the contents of two asymmetric units of the crystal structure of the bacterial serine proteinase, Streptomyces griseus proteinase A (SGPA), resulted in four dihydrogen phosphate anions migrating to form a cluster in a solvent region far removed from the protein surface. In an ef...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Blanchard H,James MN

    更新日期:1994-08-26 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


    authors: Igo MM,Losick R

    更新日期:1986-10-20 00:00:00

  • RNA binding, packaging and polymerase activities of the different incomplete polymerase complex particles of dsRNA bacteriophage phi 6.

    abstract::phi 6 is an enveloped dsRNA bacterial virus. Its segmented genome resides inside the virion associated polymerase complex which is formed by four proteins (P1, P2, P4 and P7) encoded by the viral L segment. Complete and incomplete polymerase complex particles can be produced using cDNA copies of this largest genome se...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Juuti JT,Bamford DH

    更新日期:1995-06-09 00:00:00

  • MOMP from Campylobacter jejuni Is a Trimer of 18-Stranded β-Barrel Monomers with a Ca2+ Ion Bound at the Constriction Zone.

    abstract::The Gram-negative organism Campylobacter jejuni is the major cause of food poisoning. Unlike Escherichia coli, which has two major porins, OmpC and OmpF, C. jejuni has one, termed major outer membrane protein (MOMP) through which nutrients and antibiotics transit. We report the 2.1-Å crystal structure of C. jejuni MOM...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Ferrara LGM,Wallat GD,Moynié L,Dhanasekar NN,Aliouane S,Acosta-Gutiérrez S,Pagès JM,Bolla JM,Winterhalter M,Ceccarelli M,Naismith JH

    更新日期:2016-11-06 00:00:00

  • Positive selection of synonymous mutations in vesicular stomatitis virus.

    abstract::Prevailing evolutionary forces are typically deduced from the pattern of differences in synonymous and non-synonymous mutations, under the assumption of neutrality in the absence of amino acid change. We determined the complete sequence of ten vesicular stomatitis virus populations evolving under positive selection. A...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Novella IS,Zárate S,Metzgar D,Ebendick-Corpus BE

    更新日期:2004-10-01 00:00:00

  • Purification and secondary structure determination of simian immunodeficiency virus p27.

    abstract::We have developed a novel method for the expression and purification of p27, the major core protein of simian immunodeficiency virus. Circular dichroism measurements of purified p27 were used to determine the relative amounts of alpha-helix, beta-sheet and unordered secondary structural elements. These empirically det...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Burns NR,Craig S,Lee SR,Richardsons MH,Stenner N,Adams SE,Kingsman SM,Kingsman AJ

    更新日期:1990-11-20 00:00:00

  • Order of steps in the cytochrome C folding pathway: evidence for a sequential stabilization mechanism.

    abstract::Previous work used hydrogen exchange (HX) experiments in kinetic and equilibrium modes to study the reversible unfolding and refolding of cytochrome c (Cyt c) under native conditions. Accumulated results now show that Cyt c is composed of five individually cooperative folding units, called foldons, which unfold and re...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Krishna MM,Maity H,Rumbley JN,Lin Y,Englander SW

    更新日期:2006-06-23 00:00:00

  • Nucleosome binding by the bromodomain and PHD finger of the transcriptional cofactor p300.

    abstract::The PHD finger and the bromodomain are small protein domains that occur in many proteins associated with phenomena related to chromatin. The bromodomain has been shown to bind acetylated lysine residues on histone tails. Lysine acetylation is one of several histone modifications that have been proposed to form the bas...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Ragvin A,Valvatne H,Erdal S,Arskog V,Tufteland KR,Breen K,ØYan AM,Eberharter A,Gibson TJ,Becker PB,Aasland R

    更新日期:2004-04-02 00:00:00

  • Mutant p53 in Cancer: Accumulation, Gain-of-Function, and Therapy.

    abstract::Tumor suppressor p53 plays a central role in tumor suppression. p53 is the most frequently mutated gene in human cancer, and over half of human cancers contain p53 mutations. Majority of p53 mutations in cancer are missense mutations, leading to the expression of full-length mutant p53 (mutp53) protein. While the crit...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审


    authors: Yue X,Zhao Y,Xu Y,Zheng M,Feng Z,Hu W

    更新日期:2017-06-02 00:00:00

  • PhhR binds to target sequences at different distances with respect to RNA polymerase in order to activate transcription.

    abstract::The NtrC-family PhhR protein of Pseudomonas putida is involved in the control of the metabolism of aromatic amino acids, and it is a dual regulatory protein. When PhhR acts as an activator, it stimulates transcription from its cognate promoters with RNA polymerase/sigma(70) rather than with sigma(54), as is the case f...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Herrera MC,Krell T,Zhang X,Ramos JL

    更新日期:2009-12-04 00:00:00

  • Two slow stages in refolding of bovine carbonic anhydrase B are due to proline isomerization.

    abstract::Kinetics of refolding of bovine carbonic anhydrase B have been studied by the "double-jump" technique (i.e. the dependence of protein refolding on delay time in the unfolded state after fast unfolding). It is shown that two stages (the slow with a relaxation time of t1/2 approximately equal to 120 s and the superslow ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Semisotnov GV,Uversky VN,Sokolovsky IV,Gutin AM,Razgulyaev OI,Rodionova NA

    更新日期:1990-06-05 00:00:00

  • Three-dimensional crystal structure of human eosinophil cationic protein (RNase 3) at 1.75 A resolution.

    abstract::Eosinophil cationic protein (ECP; RNase 3) is a human ribonuclease found only in eosinophil leukocytes that belongs to the RNase A superfamily. This enzyme is bactericidal, helminthotoxic and cytotoxic to mammalian cells and tissues. The protein has been cloned, heterologously overexpressed, purified and crystallized....

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Mallorquí-Fernández G,Pous J,Peracaula R,Aymamí J,Maeda T,Tada H,Yamada H,Seno M,de Llorens R,Gomis-Rüth FX,Coll M

    更新日期:2000-07-28 00:00:00

  • Kinetic analysis of the acid and the alkaline unfolded states of staphylococcal nuclease.

    abstract::Thermodynamic analysis by differential scanning calorimetry shows that the folding/unfolding transition of staphylococcal nuclease is consistent with the two-state process. Stopped-flow kinetic measurements, monitoring the Trp140 fluorescence and covering five decades in time (2 ms to 300 s), indicate that the unfoldi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Chen HM,You JL,Markin VS,Tsong TY

    更新日期:1991-08-05 00:00:00

  • Conserved structural features are found upstream from the three co-ordinately regulated discoidin I genes of Dictyostelium discoideum.

    abstract::The discoidin I genes of Dictyostelium form a small, co-ordinately regulated multigene family. We have sequenced and compared the upstream regions of the DiscI-alpha, -beta and -gamma genes. For the most part the upstream regions of the three genes are non-homologous. The upstream sequences of the beta and gamma genes...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Poole SJ,Firtel RA

    更新日期:1984-01-15 00:00:00

  • The EGF-like protein dlk1 inhibits notch signaling and potentiates adipogenesis of mesenchymal cells.

    abstract::The EGF-like homeotic gene Dlk1 appears to function as an inhibitor of adipogenesis. Overexpression of Dlk1 prevents adipogenesis of 3T3-L1 cells. Dlk1-deficient mice are obese; however, adipose tissue still develops in Fc-dlk1 transgenic mice, suggesting that Dlk1 is not a strict inhibitor of adipogenesis. To clarify...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Nueda ML,Baladrón V,Sánchez-Solana B,Ballesteros MA,Laborda J

    更新日期:2007-04-13 00:00:00

  • Identifying interacting regions in the beta subunit of Escherichia coli RNA polymerase.

    abstract::Numerous physical and genetic approaches have identified residues in the alpha, beta, beta' and sigma subunits of Escherichia coli RNA polymerase that are involved in transcriptional processes; in contrast, relatively little data exist to demonstrate interacting regions within or between the subunits themselves. As a ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Tavormina PL,Reznikoff WS,Gross CA

    更新日期:1996-05-03 00:00:00

  • Crystallization of halophilic malate dehydrogenase from Halobacterium marismortui.

    abstract::Malate dehydrogenase from the extreme halophile Halobacterium marismortui crystallizes in highly concentrated phosphate solution in space group 12 with cell dimensions a = 113.8 A, b = 122.8 A, c = 126.7 A, beta = 98.1 degrees. The halophilic enzyme was found to be unstable at lower concentrations of phosphate. It ass...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Harel M,Shoham M,Frolow F,Eisenberg H,Mevarech M,Yonath A,Sussman JL

    更新日期:1988-04-05 00:00:00