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














  • On the role of alphaThr183 in the allosteric regulation and catalytic mechanism of tryptophan synthase.

    abstract::The catalytic activity and substrate channeling of the pyridoxal 5'-phosphate-dependent tryptophan synthase alpha(2)beta(2) complex is regulated by allosteric interactions that modulate the switching of the enzyme between open, low activity and closed, high activity states during the catalytic cycle. The highly conser...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Kulik V,Weyand M,Seidel R,Niks D,Arac D,Dunn MF,Schlichting I

    更新日期:2002-12-06 00:00:00

  • Self-splicing of a Podospora anserina group IIA intron in vitro. Effects of 3'-terminal intron alterations on cleavage at the 5' and 3' splice site.

    abstract::A shortened derivative of the group IIA intron from the mitochondrial cytochrome-c-oxidase subunit I gene (COI I1) of the ascomycete Podospora anserina can undergo self-splicing in vitro. When compared to self-splicing group IIB introns from yeast mitochondria (aI5c, bI1) the autocatalytic reaction shows a lower effic...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Schmidt U,Sägebarth R,Schmelzer C,Stahl U

    更新日期:1993-06-05 00:00:00

  • Group II chaperonins: new TRiC(k)s and turns of a protein folding machine.

    abstract::In the past decade, the eubacterial group I chaperonin GroEL became the paradigm of a protein folding machine. More recently, electron microscopy and X-ray crystallography offered insights into the structure of the thermosome, the archetype of the group II chaperonins which also comprise the chaperonin from the eukary...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审


    authors: Gutsche I,Essen LO,Baumeister W

    更新日期:1999-10-22 00:00:00

  • Altered 40 S ribosomal subunits in omnipotent suppressors of yeast.

    abstract::The five suppressors SUP35, SUP43, SUP44, SUP45 and SUP46, each mapping at a different chromosomal locus in the yeast Saccharomyces cerevisiae, suppress a wide range of mutations, including representatives of all three types of nonsense mutations, UAA, UAG and UGA. We have demonstrated that ribosomes from the four sup...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Eustice DC,Wakem LP,Wilhelm JM,Sherman F

    更新日期:1986-03-20 00:00:00

  • Molecular architecture and structural transitions of a Clostridium thermocellum mini-cellulosome.

    abstract::The cellulosome is a highly elaborate cell-bound multienzyme complex that efficiently orchestrates the deconstruction of cellulose and hemicellulose, two of the nature's most abundant polymers. Understanding the intricacy of these nanomachines evolved by anaerobic microbes could sustain the development of an effective...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: García-Alvarez B,Melero R,Dias FM,Prates JA,Fontes CM,Smith SP,Romão MJ,Carvalho AL,Llorca O

    更新日期:2011-04-08 00:00:00

  • Organization of the R family and other interspersed repetitive DNA sequences in the mouse genome.

    abstract::Six R sequences have been described as members of a new family of dispersed repetitive DNA in the mouse genome (Gebhard et al., 1982). Several sequenced regions were extended in the 5' direction (R1, R2 and R6) and two new sequences were determined (R7 and R8). On the basis of our sequence and blot hybridization data ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Gebhard W,Zachau HG

    更新日期:1983-10-25 00:00:00

  • Characterization of Warfarin Inhibition Kinetics Requires Stabilization of Intramembrane Vitamin K Epoxide Reductases.

    abstract::Intramembrane enzymes are often difficult for biochemical characterization. Human vitamin K epoxide reductase (VKOR) is the target of warfarin. However, this intramembrane enzyme becomes insensitive to warfarin inhibition in vitro, preventing the characterization of inhibition kinetics for decades. Here we employ stru...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Li S,Liu S,Yang Y,Li W

    更新日期:2020-08-21 00:00:00

  • Structure of Mutant Hepatitis B Core Protein Capsids with Premature Secretion Phenotype.

    abstract::Hepatitis B virus is a major human pathogen that consists of a viral genome surrounded by an icosahedrally ordered core protein and a polymorphic, lipidic envelope that is densely packed with surface proteins. A point mutation in the core protein in which a phenylalanine at position 97 is exchanged for a smaller leuci...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Böttcher B,Nassal M

    更新日期:2018-12-07 00:00:00

  • The refined crystal structure of toxic shock syndrome toxin-1 at 2.07 A resolution.

    abstract::The pyrogenic toxin toxic shock syndrome toxin-1 from Staphylococcus aureus is a causative agent of the toxic shock syndrome disease. It belongs to a family of proteins known as superantigens that cross-link major histocompatibility class II molecules and T-cell receptors leading to the activation of a substantial num...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Papageorgiou AC,Brehm RD,Leonidas DD,Tranter HS,Acharya KR

    更新日期:1996-07-26 00:00:00

  • Shaping the Immune Landscape in Cancer by Galectin-Driven Regulatory Pathways.

    abstract::Along with the discovery of tumor-driven inflammatory pathways, there has been a considerable progress over the past 10years in understanding the mechanisms leading to cancer immunosurveillance and immunoediting. Several regulatory pathways, typically involved in immune cell homeostasis, are co-opted by cancer cells t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审


    authors: Rabinovich GA,Conejo-García JR

    更新日期:2016-08-14 00:00:00

  • Interaction of the Dengue virus fusion peptide with membranes assessed by NMR: The essential role of the envelope protein Trp101 for membrane fusion.

    abstract::Dengue virus (DV) infection depends on a step of membrane fusion, which occurs in the acidic environment of the endosome. This process is mediated by virus surface envelope glycoprotein, in which the loop between residues D98-G112 is considered to be crucial, acting as a fusion peptide. Here, we have characterized fun...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Melo MN,Sousa FJ,Carneiro FA,Castanho MA,Valente AP,Almeida FC,Da Poian AT,Mohana-Borges R

    更新日期:2009-09-25 00:00:00

  • Characterization of preferred deoxyribonuclease I cleavage sites.

    abstract::The preferred DNase I cleavage sites within the 160 bp tyrT DNA fragment were identified by studying the initial rate of cleavage of individual bonds. The results show that there is no correlation between the rate of cleavage and the identity of the dinucleotide sequence that is cleaved. Examination of the sequences s...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Herrera JE,Chaires JB

    更新日期:1994-02-18 00:00:00

  • Formation of a wrapped DNA-protein interface: experimental characterization and analysis of the large contributions of ions and water to the thermodynamics of binding IHF to H' DNA.

    abstract::To characterize driving forces and driven processes in formation of a large-interface, wrapped protein-DNA complex analogous to the nucleosome, we have investigated the thermodynamics of binding the 34-base pair (bp) H' DNA sequence to the Escherichia coli DNA-remodeling protein integration host factor (IHF). Isotherm...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Vander Meulen KA,Saecker RM,Record MT Jr

    更新日期:2008-03-14 00:00:00

  • Nucleotide sequences of immunoglobulin-epsilon pseudogenes in man and apes and their phylogenetic relationships.

    abstract::To understand the phylogenetic relationships between hominoids, the nucleotide sequences of immunoglobulin-epsilon processed pseudogenes from chimpanzee, gorilla and orangutan were determined. The basic structures of these processed pseudogenes agreed with their human counterpart. Although the degrees of nucleotide di...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Ueda S,Watanabe Y,Saitou N,Omoto K,Hayashida H,Miyata T,Hisajima H,Honjo T

    更新日期:1989-01-05 00:00:00

  • Crystal structure of Escherichia coli QOR quinone oxidoreductase complexed with NADPH.

    abstract::The crystal structure of the homodimer of quinone oxidoreductase from Escherichia coli has been determined using the multiple isomorphous replacement method at 2.2 A resolution and refined to an R-factor of 14.1% The crystallographic asymmetric unit contains one functional dimer with the two subunits being related by ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Thorn JM,Barton JD,Dixon NE,Ollis DL,Edwards KJ

    更新日期:1995-06-16 00:00:00

  • Topoisomerase II-mediated DNA cleavage: evidence for distinct regions of enzyme-DNA contacts.

    abstract::To determine the specific interaction sites of topoisomerase II within the DNA region defined by the footprint of the enzyme, we have investigated the cleavage reaction on double-stranded DNA substrates containing nicks and deletions. Topoisomerase II-mediated cleavage of the DNA substrates is suicidal as the enzyme i...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Alsner J,Sorensen HV,Schmidt VK,Sorensen BS,Westergaard O

    更新日期:1996-06-14 00:00:00

  • Dynamics of allostery in hemoglobin: roles of the penultimate tyrosine H bonds.

    abstract::The tyrosine residues adjacent to the C termini of the hemoglobin (Hb) subunits, alphaY140 and betaY145, are expected to play important structural roles, because the C termini are the loci of T-state quaternary salt-bridges, and because the tyrosine side-chains bridge the H and F helices via H bonds to the alphaV93 an...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Kneipp J,Balakrishnan G,Chen R,Shen TJ,Sahu SC,Ho NT,Giovannelli JL,Simplaceanu V,Ho C,Spiro TG

    更新日期:2006-02-17 00:00:00

  • Interactions of the natural product kendomycin and the 20S proteasome.

    abstract::Natural products are a valuable source for novel lead structures in drug discovery, but for the majority of isolated bioactive compounds, the cellular targets are unknown. The structurally unique ansa-polyketide kendomycin (KM) was reported to exert its potent cytotoxic effects via impairment of the ubiquitin proteaso...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Beck P,Heinemeyer W,Späth AL,Elnakady Y,Müller R,Groll M

    更新日期:2014-09-09 00:00:00

  • Structural evidence of a passive base-flipping mechanism for AGT, an unusual GT-B glycosyltransferase.

    abstract::The Escherichia coli T4 bacteriophage uses two glycosyltransferases to glucosylate and thus protect its DNA: the retaining alpha-glucosyltransferase (AGT) and the inverting beta-glucosyltransferase (BGT). They glucosylate 5-hydroxymethyl cytosine (5-HMC) bases of duplex DNA using UDP-glucose as the sugar donor to form...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Larivière L,Sommer N,Moréra S

    更新日期:2005-09-09 00:00:00

  • Three-dimensional structure of the complex between acyl-coenzyme A binding protein and palmitoyl-coenzyme A.

    abstract::Multidimensional 1H, 13C and 15N nuclear magnetic resonance spectroscopy has been used to study the complex between palmitoyl-coenzyme A and acyl-coenzyme A binding protein. The 1H and the 15N spectra of the holo-protein have been almost completely assigned and so has most of the 1H spectrum of the coenzyme A part of ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Kragelund BB,Andersen KV,Madsen JC,Knudsen J,Poulsen FM

    更新日期:1993-04-20 00:00:00

  • Isolation and characterization of a previously unrecognized myosin heavy chain gene present in the Syrian hamster.

    abstract::A full length (25,000 base-pair) myosin heavy chain gene completely contained within a single cosmid clone was isolated from a Syrian hamster cosmid genomic library. Sequence comparison of the 3' untranslated region indicated the presence of a 75% homology with the rat embryonic myosin heavy chain gene. Extensive 5' f...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审


    authors: McCully JD,Wang RX,Kellam B,Sole MJ,Liew CC

    更新日期:1991-04-20 00:00:00

  • Saccharomyces cerevisiae Ste50 binds the MAPKKK Ste11 through a head-to-tail SAM domain interaction.

    abstract::In Saccharomyces cerevisiae, signal transduction through pathways governing mating, osmoregulation, and nitrogen starvation depends upon a direct interaction between the sterile alpha motif (SAM) domains of the Ste11 mitogen-activated protein kinase kinase kinase (MAPKKK) and its regulator Ste50. Previously, we solved...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Kwan JJ,Warner N,Maini J,Chan Tung KW,Zakaria H,Pawson T,Donaldson LW

    更新日期:2006-02-10 00:00:00

  • Alanine scanning of MS2 coat protein reveals protein-phosphate contacts involved in thermodynamic hot spots.

    abstract::The co-crystal structure of the MS2 coat protein dimer with its RNA operator reveals eight amino acid side-chains contacting seven of the RNA phosphates. These eight amino acids and five nearby control positions were individually changed to an alanine residue and the binding affinities of the mutant proteins to the RN...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Hobson D,Uhlenbeck OC

    更新日期:2006-02-24 00:00:00

  • Molecular requirements for duplex recognition and cleavage by eukaryotic RNase III: discovery of an RNA-dependent DNA cleavage activity of yeast Rnt1p.

    abstract::Members of the double-stranded RNA (dsRNA) specific RNase III family are known to use a conserved dsRNA-binding domain (dsRBD) to distinguish RNA A-form helices from DNA B-form ones, however, the basis of this selectivity and its effect on cleavage specificity remain unknown. Here, we directly examine the molecular re...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Lamontagne B,Hannoush RN,Damha MJ,Abou Elela S

    更新日期:2004-04-23 00:00:00

  • Residues of the cytoplasmic domain of MotA essential for torque generation in the bacterial flagellar motor.

    abstract::The MotA protein of Escherichia coli is a component of the flagellum that functions, together with MotB, in transmembrane proton conduction. MotA and MotB are believed to form the stator of the flagellar motor. They are integral membrane proteins; MotA has a large (ca 22 kDa) domain in the cytoplasm, and MotB a much s...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Zhou J,Blair DF

    更新日期:1997-10-24 00:00:00

  • The three-dimensional arcitecture of the EJC core.

    abstract::The exon junction complex (EJC) is a macromolecular complex deposited at splice junctions on mRNAs as a consequence of splicing. At the core of the EJC are four proteins: eIF4AIII, a member of the DExH/D-box family of NTP-dependent RNA binding proteins, Y14, Magoh, and MLN51. These proteins form a stable heterotetrame...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Stroupe ME,Tange TØ,Thomas DR,Moore MJ,Grigorieff N

    更新日期:2006-07-21 00:00:00

  • Refined crystal structure of the catalytic domain of dihydrolipoyl transacetylase (E2p) from Azotobacter vinelandii at 2.6 A resolution.

    abstract::Dihydrolipoyl transacetylase (E2p) is both structurally and functionally the central enzyme of the pyruvate dehydrogenase multienzyme complex. The crystal structure of the catalytic domain, i.e. residues 382 to 637, of Azotobacter vinelandii E2p (E2pCD) was solved by multiple isomorphous replacement and refined by ene...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Mattevi A,Obmolova G,Kalk KH,Westphal AH,de Kok A,Hol WG

    更新日期:1993-04-20 00:00:00

  • Force-induced conformational change of bacteriorhodopsin.

    abstract::The cytoplasmic surface topography of purple membranes imaged by the atomic force microscope depends mainly on the force applied to the stylus. Imaged at forces of 300 pN, individual bacteriorhodopsin molecules reveal two domains. The resulting donut-shaped trimers reversibly transform into structures exhibiting three...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Müller DJ,Büldt G,Engel A

    更新日期:1995-06-02 00:00:00

  • Structural and functional evidence that Nck interaction with CD3epsilon regulates T-cell receptor activity.

    abstract::Recruitment of signaling molecules to the cytoplasmic domains of the CD3 subunits of the T-cell receptor (TCR) is crucial for early T-cell activation. These transient associations either do or do not require tyrosine phosphorylation of CD3 immune tyrosine activation motifs (ITAMs). Here we show that the non-ITAM-requi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Takeuchi K,Yang H,Ng E,Park SY,Sun ZY,Reinherz EL,Wagner G

    更新日期:2008-07-18 00:00:00

  • The closed MTIP-myosin A-tail complex from the malaria parasite invasion machinery.

    abstract::The Myosin A-tail interacting protein (MTIP) of the malaria parasite links the actomyosin motor of the host cell invasion machinery to its inner membrane complex. We report here that at neutral pH Plasmodium falciparum MTIP in complex with Myosin A adopts a compact conformation, with its two domains completely surroun...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Bosch J,Turley S,Roach CM,Daly TM,Bergman LW,Hol WG

    更新日期:2007-09-07 00:00:00