A branched pathway in the early stage of transcription by Escherichia coli RNA polymerase.


:The time-course of synthesis of long and short (abortive) transcripts by Escherichia coli RNA polymerase was investigated under single round conditions in vitro. The synthesis of long RNA initiated at the lambda PR (with an altered leader sequence) or at the lacUV5 promoter was completed within five minutes, but abortive transcripts were continuously synthesized for at least 20 minutes. The results indicate the presence of transcription complexes that are capable only of abortive synthesis, and not of productive elongation. Consistently, only one in four of the RNA polymerase molecules that initially associated with the lambda PR promoter synthesized long RNA. The enzyme reisolated from productive complexes synthesized both long and abortive transcripts, behaving just like the original enzyme. This suggests that RNA polymerase is homogeneous with respect to its ability to synthesize the two types of product. Overall, the results indicate that many transcription complexes can be irreversibly trapped in vitro in an abortive cycle.


J Mol Biol


Kubori T,Shimamoto N




Has Abstract


1996-03-01 00:00:00














  • Structural origins of pH and ionic strength effects on protein stability. Acid denaturation of sperm whale apomyoglobin.

    abstract::A recently developed approach to calculate the pH dependence of protein stability from three-dimensional structure information is applied to the analysis of acid denaturation of sperm whale apomyoglobin. The finite difference Poisson-Boltzmann method is used to calculate pKa values and these are used to obtain titrati...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Yang AS,Honig B

    更新日期:1994-04-15 00:00:00

  • The Bacillus subtilis and Bacillus halodurans Aspartyl-tRNA Synthetases Retain Recognition of tRNA(Asn).

    abstract::Synthesis of asparaginyl-tRNA (Asn-tRNA(Asn)) in bacteria can be formed either by directly ligating Asn to tRNA(Asn) using an asparaginyl-tRNA synthetase (AsnRS) or by synthesizing Asn on the tRNA. In the latter two-step indirect pathway, a non-discriminating aspartyl-tRNA synthetase (ND-AspRS) attaches Asp to tRNA(As...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Nair N,Raff H,Islam MT,Feen M,Garofalo DM,Sheppard K

    更新日期:2016-02-13 00:00:00

  • The critical roles of residues P235 and F236 of subunit A of the motor protein A-ATP synthase in P-loop formation and nucleotide binding.

    abstract::The mutants P235A and F236A have been generated and their crystal structure was determined to resolutions of 2.38 and 2.35 A, respectively, in order to understand the residues involved in the formation of the novel arched P-loop of subunit A of the A-ATP synthase from Pyrococcus horikoshii OT3. Both the structures sho...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Kumar A,Manimekalai MS,Balakrishna AM,Priya R,Biuković G,Jeyakanthan J,Grüber G

    更新日期:2010-09-03 00:00:00

  • The structure of Escherichia coli cytosine deaminase.

    abstract::Cytosine deaminase (CD) catalyzes the deamination of cytosine, producing uracil. This enzyme is present in prokaryotes and fungi (but not multicellular eukaryotes) and is an important member of the pyrimidine salvage pathway in those organisms. The same enzyme also catalyzes the conversion of 5-fluorocytosine to 5-flu...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Ireton GC,McDermott G,Black ME,Stoddard BL

    更新日期:2002-01-25 00:00:00

  • Phenotypic suppression by incorporation of an alien amino acid.

    abstract::Azaleucine is a naturally occurring amino acid antibiotic that can be incorporated into proteins by mimicking leucine. In spite of its highly toxic character, the contrast between the hydrophobic side-chain of leucine and the basic side-chain of azaleucine suggested a mechanism for rescuing certain mutants. We constru...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Lemeignan B,Sonigo P,Marlière P

    更新日期:1993-05-20 00:00:00

  • Crystal structure of Escherichia coli malate dehydrogenase. A complex of the apoenzyme and citrate at 1.87 A resolution.

    abstract::The crystal structure of malate dehydrogenase from Escherichia coli has been determined with a resulting R-factor of 0.187 for X-ray data from 8.0 to 1.87 A. Molecular replacement, using the partially refined structure of porcine mitochondrial malate dehydrogenase as a probe, provided initial phases. The structure of ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Hall MD,Levitt DG,Banaszak LJ

    更新日期:1992-08-05 00:00:00

  • The major surface antigens of Entamoeba histolytica trophozoites are GPI-anchored proteophosphoglycans.

    abstract::Trophozoites of the parasitic protozoa, Entamoeba histolytica, synthesize a cell surface lipoglycoconjugate, termed lipophosphoglycan, which is thought to be an important virulence factor and potential vaccine candidate against invasive amebiasis. Here, we show that the E. histolytica lipophosphoglycans are in fact gl...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Moody-Haupt S,Patterson JH,Mirelman D,McConville MJ

    更新日期:2000-03-24 00:00:00

  • Derivation of a structural model for the c-myc IRES.

    abstract::We have derived a secondary structure model for the c-myc internal ribosome entry segment (IRES) by using information from chemical probing of the c-myc IRES RNA to constrain structure prediction programs. Our data suggest that the IRES is modular in nature, and can be divided into two structural domains linked by a l...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Le Quesne JP,Stoneley M,Fraser GA,Willis AE

    更新日期:2001-06-29 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


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

    更新日期:2005-06-17 00:00:00

  • A cis-prolyl peptide bond isomerization dominates the folding of the alpha subunit of Trp synthase, a TIM barrel protein.

    abstract::The cis/trans isomerization of prolyl peptide bonds has been suggested to dominate the folding of the alpha subunit of tryptophan synthase from Escherichia coli (alphaTS). To test the role of the unique cis isomer between Asp27 and Pro28, the folding properties of P28A, P28G and G(3)P28G, a three-glycine insertion mut...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Wu Y,Matthews CR

    更新日期:2002-09-06 00:00:00

  • The structure of Antirrhinum centroradialis protein (CEN) suggests a role as a kinase regulator.

    abstract::Expression of the plant protein centroradialis (CEN) leads to a morphological switch between shoot growth and the development of flower structures (inflorescence). We have determined the crystal structure of Antirrhinum CEN to 1.9 A resolution. This structure confirms the CEN proteins as a subset of the family of phos...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Banfield MJ,Brady RL

    更新日期:2000-04-14 00:00:00

  • Jab1 mediates protein degradation of the Rad9-Rad1-Hus1 checkpoint complex.

    abstract::The Rad1-Rad9-Hus1 (9-1-1) complex serves a dual role as a DNA-damage sensor in checkpoint signaling and as a mediator in the DNA repair pathway. However, the intercellular mechanisms that regulate the 9-1-1 complex are poorly understood. Jab1, the fifth component of the COP9 signalosome complex, has a central role in...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Huang J,Yuan H,Lu C,Liu X,Cao X,Wan M

    更新日期:2007-08-10 00:00:00

  • Mapping the Allosteric Communication Network of Aminodeoxychorismate Synthase.

    abstract::Allosteric communication between different subunits in metabolic enzyme complexes is of utmost physiological importance but only understood for few systems. We analyzed the structural basis of allostery in aminodeoxychorismate synthase (ADCS), which is a member of the family of glutamine amidotransferases and catalyze...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Semmelmann F,Straub K,Nazet J,Rajendran C,Merkl R,Sterner R

    更新日期:2019-07-12 00:00:00

  • The structure of Escherichia coli nitroreductase complexed with nicotinic acid: three crystal forms at 1.7 A, 1.8 A and 2.4 A resolution.

    abstract::Escherichia coli nitroreductase is a flavoprotein that reduces a variety of quinone and nitroaromatic substrates. Its ability to convert relatively non-toxic prodrugs such as CB1954 (5-[aziridin-1-yl]-2,4-dinitrobenzamide) into highly cytotoxic derivatives has led to interest in its potential for cancer gene therapy. ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Lovering AL,Hyde EI,Searle PF,White SA

    更新日期:2001-05-25 00:00:00

  • Two types of telomeric chromatin in Tetrahymena thermophila.

    abstract::The telomeric d(GGGGTT).d(AACCCC) repeat tracts (G4T2 repeats) in Tetrahymena thermophila macronuclei were shown previously to be packaged in a non-nucleosomal DNA-protein complex. Here, we demonstrate that these telomeric repeats, together with a short region of the immediately adjacent non-telomeric sequence, exist ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Cohen P,Blackburn EH

    更新日期:1998-07-17 00:00:00

  • Phenylalanine promotes interaction of transmembrane domains via GxxxG motifs.

    abstract::Interactions of transmembrane helices play a crucial role in the folding and oligomerisation of integral membrane proteins. In order to uncover novel sequence motifs mediating these interactions, we randomised one face of a transmembrane helix with a set of non-polar or moderately polar amino acids. Those sequences ca...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Unterreitmeier S,Fuchs A,Schäffler T,Heym RG,Frishman D,Langosch D

    更新日期:2007-11-30 00:00:00

  • Quaternary structure changes in aspartate transcarbamylase studied by X-ray solution scattering. Signal transmission following effector binding.

    abstract::The result of binding the effectors ATP and CTP to aspartate transcarbamylase was studied by X-ray solution scattering. Binding of substrate analogues produces a substantial change in the solution scattering curve, allowing us to monitor the proportion of the different quaternary structure states present in solution. ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Hervé G,Moody MF,Tauc P,Vachette P,Jones PT

    更新日期:1985-09-05 00:00:00

  • Both N-Terminal and C-Terminal Histidine Residues of the Prion Protein Are Essential for Copper Coordination and Neuroprotective Self-Regulation.

    abstract::The cellular prion protein (PrPC) comprises two domains: a globular C-terminal domain and an unstructured N-terminal domain. Recently, copper has been observed to drive tertiary contact in PrPC, inducing a neuroprotective cis interaction that structurally links the protein's two domains. The location of this interacti...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Schilling KM,Tao L,Wu B,Kiblen JTM,Ubilla-Rodriguez NC,Pushie MJ,Britt RD,Roseman GP,Harris DA,Millhauser GL

    更新日期:2020-07-24 00:00:00

  • Sequence and structure-based prediction of eukaryotic protein phosphorylation sites.

    abstract::Protein phosphorylation at serine, threonine or tyrosine residues affects a multitude of cellular signaling processes. How is specificity in substrate recognition and phosphorylation by protein kinases achieved? Here, we present an artificial neural network method that predicts phosphorylation sites in independent seq...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Blom N,Gammeltoft S,Brunak S

    更新日期:1999-12-17 00:00:00

  • Different intrastrand and interstrand contributions to stacking account for roll variations at the alternating purine-pyrimidine sequences in A-DNA and A-RNA.

    abstract::An explanation is suggested for the roll alternation between low and high values in A-type nucleic acid duplexes containing alternating sequences of purine and pyrimidine residues. The explanation combines two points. (1) Roll inevitably occurs in A-type duplexes due to geometrical reasons. (2) Intrastrand base stacki...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Sponer J,Kypr J

    更新日期:1991-10-05 00:00:00

  • Predicting Protein-Protein Interfaces that Bind Intrinsically Disordered Protein Regions.

    abstract::A long-standing goal in biology is the complete annotation of function and structure on all protein-protein interactions, a large fraction of which is mediated by intrinsically disordered protein regions (IDRs). However, knowledge derived from experimental structures of such protein complexes is disproportionately sma...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Wong ETC,Gsponer J

    更新日期:2019-08-09 00:00:00

  • Translation initiation factor 3 regulates switching between different modes of ribosomal subunit joining.

    abstract::Ribosomal subunit joining is a key checkpoint in the bacterial translation initiation pathway during which initiation factors (IFs) regulate association of the 30S initiation complex (IC) with the 50S subunit to control formation of a 70S IC that can enter into the elongation stage of protein synthesis. The GTP-bound ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: MacDougall DD,Gonzalez RL Jr

    更新日期:2015-05-08 00:00:00

  • Structure, dynamics and electrostatics of the active site of glutaredoxin 3 from Escherichia coli: comparison with functionally related proteins.

    abstract::The chemistry of active-site cysteine residues is central to the activity of thiol-disulfide oxidoreductases of the thioredoxin superfamily. In these reactions, a nucleophilic thiolate is required, but the associated pK(a) values differ vastly in the superfamily, from less than 4 in DsbA to greater than 7 in Trx. The ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Foloppe N,Sagemark J,Nordstrand K,Berndt KD,Nilsson L

    更新日期:2001-07-06 00:00:00

  • Atomic force microscopy of cholera toxin B-oligomers bound to bilayers of biologically relevant lipids.

    abstract::Cholera toxin B-oligomer was imaged by atomic force microscopy (AFM) on biologically relevant model membranes, such as 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine and egg yolk phosphatidylcholine at room temperature in solution at a resolution in the range of 1 to 2 nm. In addition, two-dimensional arrays we...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Mou J,Yang J,Shao Z

    更新日期:1995-05-05 00:00:00

  • Proteasomes can degrade a significant proportion of cellular proteins independent of ubiquitination.

    abstract::The critical role of the ubiquitin-26S proteasome system in regulation of protein homeostasis in eukaryotes is well established. In contrast, the impact of the ubiquitin-independent proteolytic activity of proteasomes is poorly understood. Through biochemical analysis of mammalian lysates, we find that the 20S proteas...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Baugh JM,Viktorova EG,Pilipenko EV

    更新日期:2009-02-27 00:00:00

  • Determining the critical nucleus and mechanism of fibril elongation of the Alzheimer's Abeta(1-40) peptide.

    abstract::We use a coarse-grained protein model to characterize the critical nucleus, structural stability, and fibril elongation propensity of Abeta(1-40) oligomers for the C(2x) and C(2z) quaternary forms proposed by solid-state NMR. By estimating equilibrium populations of structurally stable and unstable protofibrils, we de...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Fawzi NL,Okabe Y,Yap EH,Head-Gordon T

    更新日期:2007-01-12 00:00:00

  • Expressed gene clusters associated with cellular sensitivity and resistance towards anti-viral and anti-proliferative actions of interferon.

    abstract::Interferons (IFN) are multi-functional proteins that induce a large number of genes which mediate many biological processes including host defense, cell growth control, signaling, and metabolism. Bioinformatics analysis of the 3'-untranslated regions of IFN-stimulated genes (ISGs) showed that the AU-rich elements (ARE...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Khabar KS,Al-Haj L,Al-Zoghaibi F,Marie M,Dhalla M,Polyak SJ,Williams BR

    更新日期:2004-09-17 00:00:00

  • Distinct Genome Replication and Transcription Strategies within the Growing Filovirus Family.

    abstract::Research on filoviruses has historically focused on the highly pathogenic ebola- and marburgviruses. Indeed, until recently, these were the only two genera in the filovirus family. Recent advances in sequencing technologies have facilitated the discovery of not only a new ebolavirus, but also three new filovirus gener...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审


    authors: Hume AJ,Mühlberger E

    更新日期:2019-10-04 00:00:00

  • Amplification of distinct subfamilies of short interspersed elements during evolution of the Salmonidae.

    abstract::There are at least three different kinds of short interspersed repetitive elements in salmonid genomes. Of these, members of the HpaI family are found to be most widely distributed in salmonid species. The HpaI family is present with high copy numbers in all members of the subfamily Salmoninae, such as salmon, trout a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章


    authors: Kido Y,Himberg M,Takasaki N,Okada N

    更新日期:1994-09-02 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


    authors: Volkov A,Jordan F

    更新日期:1996-10-11 00:00:00