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 CRP using DNase I footprinting. The functional limits of the promoters are located about 240 base-pairs (bp) upstream of their transcription start sites, which are 271 bp apart. These promoters therefore overlap by about 210 bp. The overlapping region encompasses four CRP-binding sites and at least four MalT-binding sites. Insertions in the centre of this region are tolerated provided that they correspond to an integral number of DNA helix turns. In DNase I footprinting experiments performed on the complex formed by MalT with malEp-malKp, the DNA appears to be wrapped around the protein. We propose a model for the nucleoprotein structure that might be involved in transcription activation at these divergent promoters.

journal_name

J Mol Biol

authors

Raibaud O,Vidal-Ingigliardi D,Richet E

doi

10.1016/0022-2836(89)90218-0

subject

Has Abstract

pub_date

1989-02-05 00:00:00

pages

471-85

issue

3

eissn

0022-2836

issn

1089-8638

pii

0022-2836(89)90218-0

journal_volume

205

pub_type

杂志文章
  • Folding pattern of the alpha-crystallin domain in alphaA-crystallin determined by site-directed spin labeling.

    abstract::The folding pattern of the alpha-crystallin domain, a conserved protein module encoding the molecular determinants of structure and function in the small heat-shock protein superfamily, was determined in the context of the lens protein alphaA-crystallin by systematic application of site-directed spin labeling. The seq...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3242

    authors: Koteiche HA,Mchaourab HS

    更新日期:1999-11-26 00:00:00

  • A 50th order reaction predicted and observed for sickle hemoglobin nucleation.

    abstract::Sickle hemoglobin polymerization exhibits a striking sensitivity to initial concentration, with characteristic reaction times that exhibit 30th power dependence on concentration. This extraordinary reaction order is encompassed by a novel double nucleation mechanism that predicts 50th power dependence of the homogeneo...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0079

    authors: Cao Z,Ferrone FA

    更新日期:1996-02-23 00:00:00

  • Evidence for intramolecular processing of prosubtilisin sequestered on a solid support.

    abstract::Subtilisin E is synthesized in Bacillus subtilis as a preprosubtilisin. The prepeptide is removed by a signal peptidase, and the propeptide is cleaved from the mature protein by the catalytic domain of subtilisin itself in an autocatalytic fashion. A six residue histidine-tag was attached to the C terminus of prosubti...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0538

    authors: Volkov A,Jordan F

    更新日期:1996-10-11 00:00:00

  • Core RNA polymerase and promoter DNA interactions of purified domains of sigma N: bipartite functions.

    abstract::The sigma N class of sigma factors confer upon RNA polymerase the requirement for enhancer-binding activator proteins. The sigma-N (sigma N) protein of Klebsiella pneumoniae was analysed by the assay of purified peptides comprising domains or regions of sigma N defined by proteolysis or by homology alignment, respecti...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0260

    authors: Cannon W,Missailidis S,Smith C,Cottier A,Austin S,Moore M,Buck M

    更新日期:1995-05-12 00:00:00

  • The mechanism of transcriptional activation by the topologically DNA-linked sliding clamp of bacteriophage T4.

    abstract::Three viral proteins participate directly in transcription of bacteriophage T4 late genes: the sigma-family protein gp55 provides promoter recognition, gp33 is the co-activator, and gp45 is the activator of transcription; gp33 also represses transcription in the absence of gp45. Transcriptional activation by gp45, the...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)00732-5

    authors: Kolesky SE,Ouhammouch M,Geiduschek EP

    更新日期:2002-08-30 00:00:00

  • The rate of polyQ-mediated aggregation is dramatically affected by the number and location of surrounding domains.

    abstract::The nine polyglutamine (polyQ) neurodegenerative diseases are caused in part by a gain-of-function mechanism involving protein misfolding, the deposition of β-sheet-rich aggregates and neuronal toxicity. While previous experimental evidence suggests that the polyQ-induced misfolding mechanism is context dependent, the...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.09.014

    authors: Robertson AL,Bate MA,Buckle AM,Bottomley SP

    更新日期:2011-11-04 00:00:00

  • Structural basis for oligosaccharide recognition by Pyrococcus furiosus maltodextrin-binding protein.

    abstract::A maltodextrin-binding protein from Pyrococcus furiosus (PfuMBP) has been overproduced in Escherichia coli, purified, and crystallized. The crystal structure of the protein bound to an oligosaccharide ligand was determined to 1.85 A resolution. The fold of PfuMBP is very similar to that of the orthologous MBP from E. ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.4202

    authors: Evdokimov AG,Anderson DE,Routzahn KM,Waugh DS

    更新日期:2001-01-26 00:00:00

  • Monomer and dimer of Chandipura virus unphosphorylated P-protein binds leader RNA differently: implications for viral RNA synthesis.

    abstract::Interaction of the leader RNA with the unphosphorylated P-protein has been proposed to play a key role in the transcription-replication transition of Chandipura virus, a model rhabdovirus. Electrophoretic mobility shift assay with the leader RNA and the unphosphorylated P-protein demonstrated existence of two distinct...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.03.081

    authors: Basak S,Polley S,Basu M,Chattopadhyay D,Roy S

    更新日期:2004-06-18 00:00:00

  • Dynamic Properties of Human α-Synuclein Related to Propensity to Amyloid Fibril Formation.

    abstract::α-Synuclein (αSyn) is an intrinsically disordered protein that can form amyloid fibrils. Fibrils of αSyn are implicated with the pathogenesis of Parkinson's disease and other synucleinopathies. Elucidating the mechanism of fibril formation of αSyn is therefore important for understanding the mechanism of the pathogene...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2019.05.047

    authors: Fujiwara S,Kono F,Matsuo T,Sugimoto Y,Matsumoto T,Narita A,Shibata K

    更新日期:2019-08-09 00:00:00

  • Parallel and antiparallel Holliday junctions differ in structure and stability.

    abstract::Two Holliday junction analogs, JA and JP, containing identical base-paired arms have been constructed from oligonucleotides. The former is constrained to adopt an antiparallel Sigal-Alberts structure, and the latter a parallel structure, by means of single strand d(T)9 tethers. We evaluate here the free energy differe...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)90942-y

    authors: Lu M,Guo Q,Seeman NC,Kallenbach NR

    更新日期:1991-10-20 00:00:00

  • The role of MeH73 in actin polymerization and ATP hydrolysis.

    abstract::In actin from many species H73 is methylated, but the function of this rare post-translational modification is unknown. Although not within bonding distance, it is located close to the gamma-phosphate of the actin-bound ATP. In most crystal structures of actin, the delta1-nitrogen of the methylated H73 forms a hydroge...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2002.5436

    authors: Nyman T,Schüler H,Korenbaum E,Schutt CE,Karlsson R,Lindberg U

    更新日期:2002-04-05 00:00:00

  • Structural plasticity and enzyme action: crystal structures of mycobacterium tuberculosis peptidyl-tRNA hydrolase.

    abstract::Peptidyl-tRNA hydrolase cleaves the ester bond between tRNA and the attached peptide in peptidyl-tRNA in order to avoid the toxicity resulting from its accumulation and to free the tRNA available for further rounds in protein synthesis. The structure of the enzyme from Mycobacterium tuberculosis has been determined in...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.06.053

    authors: Selvaraj M,Roy S,Singh NS,Sangeetha R,Varshney U,Vijayan M

    更新日期:2007-09-07 00:00:00

  • Visualization of protein-nucleic acid interactions in a virus. Refined structure of intact tobacco mosaic virus at 2.9 A resolution by X-ray fiber diffraction.

    abstract::The structure of tobacco mosaic virus (TMV) has been determined by fiber diffraction methods at 2.9 A resolution, and refined by restrained least-squares to an R-factor of 0.096. Protein-nucleic acid interactions are clearly visible. The final model contains all of the non-hydrogen atoms of the RNA and the protein, 71...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(89)90391-4

    authors: Namba K,Pattanayek R,Stubbs G

    更新日期:1989-07-20 00:00:00

  • The projection structure of the membrane protein microsomal glutathione transferase at 3 A resolution as determined from two-dimensional hexagonal crystals.

    abstract::The formation of two-dimensional crystals of the membrane-bound enzyme microsomal glutathione transferase is sensitive to fractional changes in the lipid-to-protein ratio. Variation of this parameter results in crystal polymorphism. The projection structure of a p6 crystal form of the enzyme has been determined by the...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2683

    authors: Schmidt-Krey I,Murata K,Hirai T,Mitsuoka K,Cheng Y,Morgenstern R,Fujiyoshi Y,Hebert H

    更新日期:1999-04-30 00:00:00

  • Electrostatic interactions in the denatured state and in the transition state for protein folding: effects of denatured state interactions on the analysis of transition state structure.

    abstract::The development of electrostatic interactions during the folding of the N-terminal domain of the ribosomal protein L9 (NTL9) is investigated by pH-dependent rate equilibrium free energy relationships. We show that Asp8, among six acidic residues, is involved in non-native, electrostatic interactions with K12 in the tr...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.04.038

    authors: Cho JH,Raleigh DP

    更新日期:2006-06-23 00:00:00

  • Photocrosslinking of benzophenone-labeled single cysteine troponin I mutants to other thin filament proteins.

    abstract::The interaction sites of rabbit skeletal troponin I (TnI) with troponin C (TnC), troponin T (TnT), tropomyosin (Tm) and actin were mapped systematically using nine single cysteine residue TnI mutants with mutation sites at positions 6, 48, 64, 89, 104, 121, 133, 155 or 179 (TnI6, TnI48 etc.). Each mutant was labeled w...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3495

    authors: Luo Y,Wu JL,Li B,Langsetmo K,Gergely J,Tao T

    更新日期:2000-02-25 00:00:00

  • Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model.

    abstract::In order to systematically analyze functionally relevant dynamical correlations within macromolecular complexes, we have developed computational methods based on the normal mode analysis of an elastic network model. First, we define two types of dynamical correlations (fluctuation-based and density-based), which are c...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.12.020

    authors: Zheng W,Brooks B

    更新日期:2005-02-25 00:00:00

  • Aromatic-aromatic interactions and protein stability. Investigation by double-mutant cycles.

    abstract::The side-chains of phenylalanine and tyrosine residues in proteins are frequently found to be involved in pairwise interactions. These occur both within repeating elements of secondary structure and in tertiary and quaternary interactions. It has been suggested that they are important in protein folding and stability,...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)90725-l

    authors: Serrano L,Bycroft M,Fersht AR

    更新日期:1991-03-20 00:00:00

  • Crystal structures of an oligopeptide-binding protein from the biosynthetic pathway of the beta-lactamase inhibitor clavulanic acid.

    abstract::Clavulanic acid (CA) is a clinically important beta-lactamase inhibitor that is produced by fermentation of Streptomyces clavuligerus. The CA biosynthesis pathway starts from arginine and glyceraldehyde-3-phosphate and proceeds via (3S,5S)-clavaminic acid, which is converted to (3R,5R)-clavaldehyde, the immediate prec...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.11.045

    authors: Mackenzie AK,Valegård K,Iqbal A,Caines ME,Kershaw NJ,Jensen SE,Schofield CJ,Andersson I

    更新日期:2010-02-19 00:00:00

  • Protein oligomerization through domain swapping: role of inter-molecular interactions and protein concentration.

    abstract::Domain swapping has been shown to be an important mechanism controlling multiprotein assembly and has been suggested recently as a possible mechanism underlying protein aggregation. Understanding oligomerization via domain swapping is therefore of theoretical and practical importance. By using a symmetrized structure-...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.06.062

    authors: Yang S,Levine H,Onuchic JN

    更新日期:2005-09-09 00:00:00

  • Structures of the TetR-like simocyclinone efflux pump repressor, SimR, and the mechanism of ligand-mediated derepression.

    abstract::Simocyclinone D8 (SD8), a potent DNA gyrase inhibitor made by Streptomyces antibioticus, is exported from the producing organism by the SimX efflux pump. The expression of simX is under the control of SimR, a member of the TetR family of transcriptional regulators. SimR represses simX transcription by binding to opera...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.02.035

    authors: Le TB,Stevenson CE,Fiedler HP,Maxwell A,Lawson DM,Buttner MJ

    更新日期:2011-04-22 00:00:00

  • The 1.5 A crystal structure of a bleomycin resistance determinant from bleomycin-producing Streptomyces verticillus.

    abstract::Bleomycin (Bm)-binding protein, designated BLMA, which is a Bm resistance determinant from Bm-producing Streptomyces verticillus, was crystallized in a form suitable for X-ray diffraction analysis. The diffraction intensity data were collected up to a resolution of 1.5 A with a merging R-value of 0.054 at a completene...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3404

    authors: Kawano Y,Kumagai T,Muta K,Matoba Y,Davies J,Sugiyama M

    更新日期:2000-01-28 00:00:00

  • Solution dynamics of the trp repressor: a study of amide proton exchange by T1 relaxation.

    abstract::The amide proton exchange rates of Escherichia coli trp repressor have been measured through their effects on the longitudinal relaxation rates of the amide protons. Three types of exchange regimes have been observed: (1) slow exchange (on a minute/hour time-scale), measurable by isotope exchange, but not by relaxatio...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(05)80111-1

    authors: Gryk MR,Finucane MD,Zheng Z,Jardetzky O

    更新日期:1995-03-10 00:00:00

  • Towards the molecular architecture of the asymmetric unit membrane of the mammalian urinary bladder epithelium: a closed "twisted ribbon" structure.

    abstract::The asymmetric unit membrane (AUM) forms numerous plaques covering the apical surface of mammalian urinary bladder epithelium. These plaques contain four major integral membrane proteins called uroplakins Ia, Ib, II and III, which form particles arranged in a well-ordered hexagonal lattice with p6 symmetry and a latti...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0269

    authors: Walz T,Häner M,Wu XR,Henn C,Engel A,Sun TT,Aebi U

    更新日期:1995-05-19 00:00:00

  • Structural basis for the dual recognition of IL-12 and IL-23 by ustekinumab.

    abstract::Interleukin (IL)-12 and IL-23 are heterodimeric proinflammatory cytokines that share a common p40 subunit, paired with p35 and p19 subunits, respectively. They represent an attractive class of therapeutic targets for the treatment of psoriasis and other immune-mediated diseases. Ustekinumab is a fully human monoclonal...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.07.046

    authors: Luo J,Wu SJ,Lacy ER,Orlovsky Y,Baker A,Teplyakov A,Obmolova G,Heavner GA,Richter HT,Benson J

    更新日期:2010-10-08 00:00:00

  • Bacterial repression loops require enhanced DNA flexibility.

    abstract::The Escherichia coli lac operon provides a classic paradigm for understanding regulation of gene transcription. It is now appreciated that lac promoter repression involves cooperative binding of the bidentate lac repressor tetramer to pairs of lac operators via DNA looping. We have adapted components of this system to...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.04.035

    authors: Becker NA,Kahn JD,Maher LJ 3rd

    更新日期:2005-06-17 00:00:00

  • Analysis of the relationship between side-chain conformation and secondary structure in globular proteins.

    abstract::The relationship between the preferred side-chain dihedral angles and the secondary structure of a residue was examined. The structures of 61 proteins solved to a resolution of 2.0 A (1 A = 0.1 nm) or better were analysed using a relational database to store the information. The strongest feature observed was that the...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(87)90314-7

    authors: McGregor MJ,Islam SA,Sternberg MJ

    更新日期:1987-11-20 00:00:00

  • Structure of adenovirus fibre. I. Analysis of crystals of fibre from adenovirus serotypes 2 and 5 by electron microscopy and X-ray crystallography.

    abstract::An analysis by electron microscopy in amorphous ice and X-ray diffraction of four types of three-dimensional crystals of adenovirus fibre is presented. Fibre from adenovirus type 2 (Ad2) crystallizes in two forms depending on whether it is native or cleaved near the N terminus at Tyr17. Fibre from Ad5 also crystallize...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/S0022-2836(05)80169-X

    authors: Devaux C,Adrian M,Berthet-Colominas C,Cusack S,Jacrot B

    更新日期:1990-10-20 00:00:00

  • High-resolution crystal structures of Drosophila melanogaster angiotensin-converting enzyme in complex with novel inhibitors and antihypertensive drugs.

    abstract::Angiotensin I-converting enzyme (ACE), one of the central components of the renin-angiotensin system, is a key therapeutic target for the treatment of hypertension and cardiovascular disorders. Human somatic ACE (sACE) has two homologous domains (N and C). The N- and C-domain catalytic sites have different activities ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2010.05.024

    authors: Akif M,Georgiadis D,Mahajan A,Dive V,Sturrock ED,Isaac RE,Acharya KR

    更新日期:2010-07-16 00:00:00

  • A New Type of Circular RNA derived from Nonconventional Introns in Nuclear Genes of Euglenids.

    abstract::Nuclear protein-coding genes of euglenids (Discoba, Euglenozoa, Euglenida) contain conventional (spliceosomal) and nonconventional introns. The latter have been found only in euglenozoans. A unique feature of nonconventional introns is the ability to form a stable and slightly conserved RNA secondary structure bringin...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2020.166758

    authors: Gumińska N,Zakryś B,Milanowski R

    更新日期:2021-02-05 00:00:00