Leucine-induced dissociation of Escherichia coli Lrp hexadecamers to octamers.

Abstract:

:Lrp is a global regulator of metabolism in Escherichia coli that helps cells respond to changes in environmental conditions. The action of Lrp as a transcriptional activator or repressor is sometimes affected when the medium contains exogenous leucine. In this study, we examined the thermodynamics of leucine binding to Lrp and to a leucine response mutant, Lrp-1, and leucine-induced dissociation of Lrp hexadecamer to leucine-bound octamer. The results of dynamic light-scattering and fluorescence measurements suggest that Lrp has two leucine-binding sites, one a high-affinity site and the other a low-affinity site that is coupled to the dissociation reaction. The Gibbs free energy change for leucine binding to the high-affinity site is about -7.0 kcal/mol. Binding of two leucine molecules to low-affinity sites on the hexadecamer or one leucine molecule to one octamer induces the dissociation of hexadecamer to leucine-bound octamer. The Gibbs free energy change for leucine binding to the low-affinity site was estimated to be in the range -4.66 to -5.03 kcal/mol for leucine binding to an octamer or -6.01 to -6.75 kcal/mol for leucine binding to a hexadecamer. The thermodynamic parameters derived from this study were used together with other data to estimate the distribution of free Lrp hexadecamer, octamer, leucine-bound hexadecamer, and leucine-bound octamer in cells. Mathematical modeling, employed to simulate modulation of Lrp action in response to growth conditions, gave results that are consistent with known patterns of Lrp action on different operons.

journal_name

J Mol Biol

authors

Chen S,Calvo JM

doi

10.1016/S0022-2836(02)00187-0

keywords:

subject

Has Abstract

pub_date

2002-05-10 00:00:00

pages

1031-42

issue

4

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(02)00187-0

journal_volume

318

pub_type

杂志文章
  • Negatively stained 50 S ribosomal subunits of Escherichia coli.

    abstract::Ribosomes are large nucleoproteins of approximately 3 X 10(6) Mr. In contrast to helical or spherical nucleoproteins (viruses) of similar size (which consist of several hundred small asymmetric units reproduced by symmetry), ribosomes are completely asymmetric; therefore, the amount of structural information (defined ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(86)90366-9

    authors: Hoppe W,Oettl H,Tietz HR

    更新日期:1986-11-20 00:00:00

  • Crystallization and preliminary X-ray crystallographic studies of thermostable xylanase crystals isolated from Paecilomyces varioti.

    abstract::A highly thermostable xylanase isolated from the thermophilic fungus Paecilomyces varioti has been crystallized by the vapour diffusion method. The isolation of this enzyme by crystallization directly from the culture filtrate projects this fungus as an important source for large-scale production of pure xylanase. The...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(94)90052-3

    authors: Eswaramoorthy S,Vithayathil PJ,Viswamitra MA

    更新日期:1994-11-04 00:00:00

  • Crystal structure of Escherichia coli thioesterase I/protease I/lysophospholipase L1: consensus sequence blocks constitute the catalytic center of SGNH-hydrolases through a conserved hydrogen bond network.

    abstract::Escherichia coli thioesterase I (TAP) is a multifunctional enzyme possessing activities of thioesterase, esterase, arylesterase, protease, and lysophospholipase. In particular, TAP has stereoselectivity for amino acid derivative substrates, hence it is useful for the kinetic resolution of racemic mixtures of industria...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(03)00637-5

    authors: Lo YC,Lin SC,Shaw JF,Liaw YC

    更新日期:2003-07-11 00:00:00

  • A single tyrosine prevents insertion of ribonucleotides in the eukaryotic-type phi29 DNA polymerase.

    abstract::Three conserved motifs (named A, B and C) have been proposed to form the polymerization active site in all classes of DNA-dependent polymerases. In eukaryotic-type (alpha-like) DNA polymerases, motif A is characterized by the consensus "Dx2SLYP". Mutants in phi29 DNA polymerase residue Tyr254 of this conserved motif h...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2900

    authors: Bonnin A,Lázaro JM,Blanco L,Salas M

    更新日期:1999-07-02 00:00:00

  • X-ray diffraction analysis of crystals of bovine platelet factor 4.

    abstract::Bovine platelet factor 4 has been crystallized by "vapor dilution" in space group P2(1)2(1)2(1), a = 63.7 A, b = 66.7 A, c = 80.5 A, with four molecules, each 9505 Mr, in the asymmetric unit. The crystals diffract X-rays to better than 2.8 A resolution. ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(84)90497-2

    authors: St Charles R,Ciaglowski RE,Walz D,Edwards BF

    更新日期:1984-07-05 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

    doi:10.1016/0022-2836(91)90116-n

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

    更新日期:1991-08-05 00:00:00

  • Structural studies of the final enzyme in the alpha-aminoadipate pathway-saccharopine dehydrogenase from Saccharomyces cerevisiae.

    abstract::The 1.64 A structure of the apoenzyme form of saccharopine dehydrogenase (SDH) from Saccharomyces cerevisiae shows the enzyme to be composed of two domains with similar dinucleotide binding folds with a deep cleft at the interface. The structure reveals homology to alanine dehydrogenase, despite low primary sequence s...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.08.044

    authors: Burk DL,Hwang J,Kwok E,Marrone L,Goodfellow V,Dmitrienko GI,Berghuis AM

    更新日期:2007-10-26 00:00:00

  • Intracellular antibody capture technology: application to selection of intracellular antibodies recognising the BCR-ABL oncogenic protein.

    abstract::The expression of antibodies inside cells to ablate protein function has the potential for disease therapy and for target validation in functional genomics. However, due to inefficient expression or folding, only a few antibodies or antibody fragments, usually as single-chain Fv antibody fragments (scFv), bind their a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2002.5403

    authors: Tse E,Lobato MN,Forster A,Tanaka T,Chung GT,Rabbitts TH

    更新日期:2002-03-15 00:00:00

  • Visualization and exact molecular weight determination of a Rhizobium meliloti megaplasmid.

    abstract::The entire DNA of Rhizobium meliloti MVII /1 cells was isolated preparatively by gentle lysis and sucrose gradient centrifugation. Fractions of the sucrose gradient were investigated by electron microscopy. We found intact megaplasmids in supercoiled and relaxed form and total chromosomes. The length of the megaplasmi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(84)90475-3

    authors: Burkardt B,Burkardt HJ

    更新日期:1984-05-15 00:00:00

  • Location of the SH group of the alkali light chain on the myosin head as revealed by electron microscopy.

    abstract::The location of the single cysteinyl residue of the alkali light chain on the myosin head was determined by electron microscopy. The cysteinyl residue of isolated alkali light chain 2 was biotinylated and the light chain was exchanged with that of heavy meromyosin in 4.7 M-NH4Cl. Avidin was attached to the biotin in t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(85)90222-0

    authors: Yamamoto K,Tokunaga M,Sutoh K,Wakabayashi T,Sekine T

    更新日期:1985-05-25 00:00:00

  • Weighting aligned protein or nucleic acid sequences to correct for unequal representation.

    abstract::Aligned sequences from the same family (e.g. the haemoglobins) are seldom representative of the entire family. This is because (1) the sequence databases are heavily skewed toward a small number of organisms and (2) only a minute fraction of all the different family members have been sequenced. For many applications, ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/S0022-2836(99)80003-5

    authors: Sibbald PR,Argos P

    更新日期:1990-12-20 00:00:00

  • Antisense-RNA mediated transcriptional attenuation: importance of a U-turn loop structure in the target RNA of plasmid pIP501 for efficient inhibition by the antisense RNA.

    abstract::Antisense-RNA mediated gene regulation has been found and studied in detail mainly in prokaryotic accessory DNA elements. In spite of different regulatory mechanisms, in all cases a rapid interaction between antisense and target RNA has been shown to be crucial for efficient regulation. Recently, a sequence comparison...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2003.09.020

    authors: Heidrich N,Brantl S

    更新日期:2003-11-07 00:00:00

  • Pentameric and decameric structures in solution of serum amyloid P component by X-ray and neutron scattering and molecular modelling analyses.

    abstract::Human serum amyloid P component (SAP) is a normal plasma glycoprotein and the precursor of amyloid P component which is a universal constituent of the abnormal tissue deposits in amyloidosis. X-ray and neutron scattering data showed that pentameric or decameric ring structures for SAP in solution are readily distingui...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.1271

    authors: Ashton AW,Boehm MK,Gallimore JR,Pepys MB,Perkins SJ

    更新日期:1997-09-26 00:00:00

  • 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 ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2016.10.015

    authors: Chan RT,Keating KS,Go MC,Toor N

    更新日期:2016-12-04 00:00:00

  • High affinity cooperative DNA binding by the yeast Mlh1-Pms1 heterodimer.

    abstract::We demonstrate here that the Saccharomyces cerevisiae Mlh1-Pms1 heterodimer required for DNA mismatch repair and other cellular processes is a DNA binding protein. Binding was evaluated using a variety of single and double-stranded DNA molecules. Mlh1-Pms1 bound short substrates with low affinity and showed a slight p...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4958

    authors: Hall MC,Wang H,Erie DA,Kunkel TA

    更新日期:2001-09-28 00:00:00

  • Prohead and DNA-gp3-dependent ATPase activity of the DNA packaging protein gp16 of bacteriophage phi 29.

    abstract::The ATPase activity of the DNA packaging protein gp16 (gene product 16) of bacteriophage phi 29 was studied in the completely defined in-vitro assembly system. ATP was hydrolyzed to ADP and Pi in the packaging reaction that included purified proheads, DNA-gp3 and gp16. Approximately one molecule of ATP was used in the...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(87)90121-5

    authors: Guo P,Peterson C,Anderson D

    更新日期:1987-09-20 00:00:00

  • Human prorenin structure sheds light on a novel mechanism of its autoinhibition and on its non-proteolytic activation by the (pro)renin receptor.

    abstract::Antibodies and prorenin mutants have long been used to structurally characterize prorenin, the inactive proenzyme form of renin. They were designed on the basis of homology models built using other aspartyl protease proenzyme structures since no structure was available for prorenin. Here, we present the first X-ray st...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2012.05.003

    authors: Morales R,Watier Y,Böcskei Z

    更新日期:2012-08-03 00:00:00

  • Changes in side-chain and backbone dynamics identify determinants of specificity in RNA recognition by human U1A protein.

    abstract::The ribonucleoprotein (RNP) domain is one of the most common eukaryotic protein domains, and is found in many proteins involved in recognition of a wide variety of RNAs. Two structures of RNA complexes of human U1A protein have revealed important aspects of RNP-RNA recognition, but have also raised intriguing question...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3311

    authors: Mittermaier A,Varani L,Muhandiram DR,Kay LE,Varani G

    更新日期:1999-12-10 00:00:00

  • An EM view of the FokI synaptic complex by single particle analysis.

    abstract::FokI is a type IIS restriction endonuclease that recognizes the 5'-GGATG-3' sequence and cleaves non-specifically at 9 and 13 base-pairs away on the top and bottom strands, respectively, to produce a 5' overhang. FokI is a bipartite endonuclease with separate recognition and cleavage domains. Because of its bipartite ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.04.066

    authors: Vanamee ES,Berriman J,Aggarwal AK

    更新日期:2007-07-06 00:00:00

  • Improving profile HMM discrimination by adapting transition probabilities.

    abstract::Profile hidden Markov models (HMMs) are used to model protein families and for detecting evolutionary relationships between proteins. Such a profile HMM is typically constructed from a multiple alignment of a set of related sequences. Transition probability parameters in an HMM are used to model insertions and deletio...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.03.023

    authors: Wistrand M,Sonnhammer EL

    更新日期:2004-05-07 00:00:00

  • Crystal structure of the three tandem FF domains of the transcription elongation regulator CA150.

    abstract::FF domains are small protein-protein interaction modules that have two flanking conserved phenylalanine residues. They are present in proteins involved in transcription, RNA splicing, and signal transduction, and often exist in tandem arrays. Although several individual FF domain structures have been determined by NMR...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.07.086

    authors: Lu M,Yang J,Ren Z,Sabui S,Espejo A,Bedford MT,Jacobson RH,Jeruzalmi D,McMurray JS,Chen X

    更新日期:2009-10-23 00:00:00

  • Regulation of IS1 transposition by the insA gene product.

    abstract::The IS1 element contains two adjacent genes called insA and insB, both required for IS1 transposition and IS1-mediated plasmid cointegration. These two genes are transcribed polycistronically from the promoter in the left terminal inverted repeat of IS1 (insL). We constructed overexpression systems of these genes with...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(89)90148-4

    authors: Machida C,Machida Y

    更新日期:1989-08-20 00:00:00

  • Molecular characterisation of aureocin A70, a multi-peptide bacteriocin isolated from Staphylococcus aureus.

    abstract::Staphylococcus aureus A70 produces a heat-stable bacteriocin designated aureocin A70. Aureocin A70 is encoded within a mobilisable 8 kb plasmid, pRJ6, and is active against Listeria monocytogenes. Experiments of transposition mutagenesis and gene cloning had shown that aureocin A70 production and immunity were associa...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4885

    authors: Netz DJ,Sahl HG,Marcelino R,dos Santos Nascimento J,de Oliveira SS,Soares MB,do Carmo de Freire Bastos M

    更新日期:2001-08-31 00:00:00

  • Structural comparison of cuticle and interstitial collagens from annelids living in shallow sea-water and at deep-sea hydrothermal vents.

    abstract::Two types of annelid collagens of different sizes were purified, one from acetic acid extracts of the cuticle (length 2.5 microns) and the other, after pepsin digestion, from interstitial spaces of the body wall (0.3 micron). They were obtained from Alvinella pompejana, Alvinella caudata and Paralvinella grasslei coll...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.0084

    authors: Gaill F,Mann K,Wiedemann H,Engel J,Timpl R

    更新日期:1995-02-17 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

    doi:10.1016/j.jmb.2006.10.043

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

    更新日期:2007-04-13 00:00:00

  • Crystal structure of the factor for inversion stimulation FIS at 2.0 A resolution.

    abstract::The factor for inversion stimulation (FIS) binds as a homodimeric molecule to a loose 15 nucleotide consensus sequence in DNA. It stimulates DNA-related processes, such as DNA inversion and excision, it activates transcription of tRNA and rRNA genes and it regulates its own synthesis. FIS crystallizes as a homodimer, ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(92)90134-6

    authors: Kostrewa D,Granzin J,Stock D,Choe HW,Labahn J,Saenger W

    更新日期:1992-07-05 00:00:00

  • Crystal Structure of a Complex of the Intracellular Domain of Interferon λ Receptor 1 (IFNLR1) and the FERM/SH2 Domains of Human JAK1.

    abstract::The crystal structure of a construct consisting of the FERM and SH2-like domains of the human Janus kinase 1 (JAK1) bound to a fragment of the intracellular domain of the interferon-λ receptor 1 (IFNLR1) has been determined at the nominal resolution of 2.1Å. In this structure, the receptor peptide forms an 85-Å-long e...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2016.10.005

    authors: Zhang D,Wlodawer A,Lubkowski J

    更新日期:2016-11-20 00:00:00

  • Characterization of hnRNP K protein-RNA interactions.

    abstract::The heterogeneous nuclear ribonucleoprotein K protein is an RNA-binding protein found in several subcellular compartments where it is thought to be involved in signaling multiple processes that compose gene expression. K protein contains three K homology (KH) domains that mediate RNA-binding. We used a serial analysis...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.07.099

    authors: Klimek-Tomczak K,Wyrwicz LS,Jain S,Bomsztyk K,Ostrowski J

    更新日期:2004-09-24 00:00:00

  • NMR structure of the integral membrane protein OmpX.

    abstract::The structure of the integral membrane protein OmpX from Escherichia coli reconstituted in 60 kDa DHPC micelles (OmpX/DHPC) was calculated from 526 NOE upper limit distance constraints. The structure determination was based on complete sequence-specific assignments for the amide protons and the Val, Leu, and Ile(delta...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2003.09.014

    authors: Fernández C,Hilty C,Wider G,Güntert P,Wüthrich K

    更新日期:2004-03-05 00:00:00

  • Functional regions and structural features of the gB glycoprotein of herpes simplex virus type 1. An analysis of linker insertion mutants.

    abstract::Glycoprotein B (gB) of Herpes simplex virus type 1 (HSV-1) plays an essential role in viral entry. A set of more than 100 HpaI (GTTAAC) linker insertion mutations and their derivatives were isolated in plasmids specifying the gB coding and flanking sequences. Mutations including addition, deletion and nonsense mutatio...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(88)90639-0

    authors: Cai WZ,Person S,DebRoy C,Gu BH

    更新日期:1988-06-05 00:00:00