Crystal structure of yeast TATA-binding protein and model for interaction with DNA.

Abstract:

:The C-terminal 179-aa region of yeast (Saccharomyces cerevisiae) TATA-binding protein (TBP), phylogenetically conserved and sufficient for many functions, formed crystals diffracting to 1.7-A resolution. The structure of the protein, determined by molecular replacement with coordinates from Arabidopsis TBP and refined to 2.6 A, differed from that in Arabidopsis slightly by an angle of about 12 degrees between two structurally nearly identical subdomains, indicative of a degree of conformational flexibility. A model for TBP-DNA interaction is proposed with the following important features: the long dimension of the protein follows the trajectory of the minor groove; two rows of basic residues conserved between the subdomains lie along the edges of the protein in proximity to the DNA phosphates; a band of hydrophobic residues runs down the middle of the groove; and amino acid residues whose mutation alters specificity for the second base of the TATA sequence are juxtaposed to that base.

authors

Chasman DI,Flaherty KM,Sharp PA,Kornberg RD

doi

10.1073/pnas.90.17.8174

subject

Has Abstract

pub_date

1993-09-01 00:00:00

pages

8174-8

issue

17

eissn

0027-8424

issn

1091-6490

journal_volume

90

pub_type

杂志文章
  • Nerve growth factor stimulates protein tyrosine phosphorylation in PC-12 pheochromocytoma cells.

    abstract::The cellular actions of nerve growth factor (NGF) and epidermal growth factor (EGF) may be mediated by changes in protein phosphorylation. The tyrosine phosphorylation of two predominant proteins of molecular mass 40 and 42 kDa is seen in PC-12 cells treated with NGF or EGF, correlating with activation of a previously...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.88.7.2653

    authors: Miyasaka T,Sternberg DW,Miyasaka J,Sherline P,Saltiel AR

    更新日期:1991-04-01 00:00:00

  • The role of charge and multiple faces of the CD8 alpha/alpha homodimer in binding to major histocompatibility complex class I molecules: support for a bivalent model.

    abstract::The CD8 dimer interacts with the alpha 3 domain of major histocompatibility complex class I molecules through two immunoglobulin variable-like domains. In this study a crystal structure-informed mutational analysis has been performed to identify amino acids in the CD8 alpha/alpha homodimer that are likely to be involv...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.91.5.1716

    authors: Giblin PA,Leahy DJ,Mennone J,Kavathas PB

    更新日期:1994-03-01 00:00:00

  • Policy folklists and evolutionary theory.

    abstract::Policy folklists present a set of alleged historical facts seen as relevant to some social issue. Although the validity of these folklists is dubious, leaders and writers circulate them in the media, variants arise, and the lists continue on, sometimes for decades. Folklists are repeated because their messages are app...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1402959111

    authors: O'Neill B

    更新日期:2014-07-22 00:00:00

  • Cytoplasmic transfer of resistance to antimycin A in Chinese hamster cells.

    abstract::A mutant subline of V79 Chinese hamster cells resistant to antimycin A (ANT) was obtained by treatment with ethyl methanesulfonate followed by serial selection in ANT-containing medium. Clonal derivatives of the resistant line are less susceptible than parent cells to growth inhibition by ANT in mass populations and s...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.75.11.5604

    authors: Harris M

    更新日期:1978-11-01 00:00:00

  • The osmolyte xylitol reduces the salt concentration of airway surface liquid and may enhance bacterial killing.

    abstract::The thin layer of airway surface liquid (ASL) contains antimicrobial substances that kill the small numbers of bacteria that are constantly being deposited in the lungs. An increase in ASL salt concentration inhibits the activity of airway antimicrobial factors and may partially explain the pathogenesis of cystic fibr...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.97.21.11614

    authors: Zabner J,Seiler MP,Launspach JL,Karp PH,Kearney WR,Look DC,Smith JJ,Welsh MJ

    更新日期:2000-10-10 00:00:00

  • Experience versus talent shapes the structure of the Web.

    abstract::We use sequential large-scale crawl data to empirically investigate and validate the dynamics that underlie the evolution of the structure of the web. We find that the overall structure of the web is defined by an intricate interplay between experience or entitlement of the pages (as measured by the number of inbound ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0805921105

    authors: Kong JS,Sarshar N,Roychowdhury VP

    更新日期:2008-09-16 00:00:00

  • Genetic heterogeneity in ataxia-telangiectasia studied by cell fusion.

    abstract::The effect of x-rays on the rate of semiconservative DNA replication was investigated by autoradiography in single cells obtained from normal individuals and from patients having ataxia-telangiectasia (AT). In the five AT cell strains studied, the rate of DNA synthesis was inhibited to a lesser extent that in two norm...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.79.8.2641

    authors: Jaspers NG,Bootsma D

    更新日期:1982-04-01 00:00:00

  • Insulin receptors in beta-cells are critical for islet compensatory growth response to insulin resistance.

    abstract::Insulin and insulin-like growth factor 1 (IGF1) are ubiquitous growth factors that regulate proliferation in most mammalian tissues including pancreatic islets. To explore the specificity of insulin receptors in compensatory beta-cell growth, we examined two models of insulin resistance. In the first model, we used li...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0608703104

    authors: Okada T,Liew CW,Hu J,Hinault C,Michael MD,Krtzfeldt J,Yin C,Holzenberger M,Stoffel M,Kulkarni RN

    更新日期:2007-05-22 00:00:00

  • "Real-time" obstacle avoidance in the absence of primary visual cortex.

    abstract::When we reach toward objects, we easily avoid potential obstacles located in the workspace. Previous studies suggest that obstacle avoidance relies on mechanisms in the dorsal visual stream in the posterior parietal cortex. One fundamental question that remains unanswered is where the visual inputs to these dorsal-str...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0905549106

    authors: Striemer CL,Chapman CS,Goodale MA

    更新日期:2009-09-15 00:00:00

  • Alpha-helices direct excitation energy flow in the Fenna Matthews Olson protein.

    abstract::In photosynthesis, light is captured by antenna proteins. These proteins transfer the excitation energy with almost 100% quantum efficiency to the reaction centers, where charge separation takes place. The time scale and pathways of this transfer are controlled by the protein scaffold, which holds the pigments at opti...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0708222104

    authors: Müh F,Madjet Mel-A,Adolphs J,Abdurahman A,Rabenstein B,Ishikita H,Knapp EW,Renger T

    更新日期:2007-10-23 00:00:00

  • Coexpression of NOS2 and COX2 accelerates tumor growth and reduces survival in estrogen receptor-negative breast cancer.

    abstract::Proinflammatory signaling pathways are commonly up-regulated in breast cancer. In estrogen receptor-negative (ER-) and triple-negative breast cancer (TNBC), nitric oxide synthase-2 (NOS2) and cyclooxygenase-2 (COX2) have been described as independent predictors of disease outcome. We further explore these findings by ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1709119114

    authors: Basudhar D,Glynn SA,Greer M,Somasundaram V,No JH,Scheiblin DA,Garrido P,Heinz WF,Ryan AE,Weiss JM,Cheng RYS,Ridnour LA,Lockett SJ,McVicar DW,Ambs S,Wink DA

    更新日期:2017-12-05 00:00:00

  • Identification of IL-17-producing FOXP3+ regulatory T cells in humans.

    abstract::IL-17-producing CD4(+) T helper (Th17) cells have recently been defined as a unique subset of proinflammatory helper cells whose development depends on signaling initiated by IL-6 and TGF-beta, autocrine activity of IL-21, activation of STAT3, and induction of the orphan nuclear receptor RORgammat. The maintenance, ex...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0900408106

    authors: Voo KS,Wang YH,Santori FR,Boggiano C,Wang YH,Arima K,Bover L,Hanabuchi S,Khalili J,Marinova E,Zheng B,Littman DR,Liu YJ

    更新日期:2009-03-24 00:00:00

  • Cathepsin B: association with plasma membrane in metastatic tumors.

    abstract::The subcellular localization of cathepsin B activity (EC 3.4.22.1) in three murine melanomas of increasing metastatic potential (Cloudman less than B16-F1 less than B16 amelanotic) was determined. Cathepsin B activity was localized in the heavy mitochondrial fraction of normal murine liver but in the light mitochondri...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.83.8.2483

    authors: Sloane BF,Rozhin J,Johnson K,Taylor H,Crissman JD,Honn KV

    更新日期:1986-04-01 00:00:00

  • Unifying account of visual motion and position perception.

    abstract::Despite growing evidence for perceptual interactions between motion and position, no unifying framework exists to account for these two key features of our visual experience. We show that percepts of both object position and motion derive from a common object-tracking system--a system that optimally integrates sensory...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1500361112

    authors: Kwon OS,Tadin D,Knill DC

    更新日期:2015-06-30 00:00:00

  • Modeling gene and genome duplications in eukaryotes.

    abstract::Recent analysis of complete eukaryotic genome sequences has revealed that gene duplication has been rampant. Moreover, next to a continuous mode of gene duplication, in many eukaryotic organisms the complete genome has been duplicated in their evolutionary past. Such large-scale gene duplication events have been assoc...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0501102102

    authors: Maere S,De Bodt S,Raes J,Casneuf T,Van Montagu M,Kuiper M,Van de Peer Y

    更新日期:2005-04-12 00:00:00

  • Dietary branched chain amino acids ameliorate injury-induced cognitive impairment.

    abstract::Neurological dysfunction caused by traumatic brain injury results in profound changes in net synaptic efficacy, leading to impaired cognition. Because excitability is directly controlled by the balance of excitatory and inhibitory activity, underlying mechanisms causing these changes were investigated using lateral fl...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0910280107

    authors: Cole JT,Mitala CM,Kundu S,Verma A,Elkind JA,Nissim I,Cohen AS

    更新日期:2010-01-05 00:00:00

  • Factors affecting counteraction by methylamines of urea effects on aldose reductase.

    abstract::The concentration of urea in renal medullary cells is high enough to affect enzymes seriously by reducing Vmax or raising Km, yet the cells survive and function. The usual explanation is that the methylamines found in the renal medulla, namely glycerophosphocholine and betaine, have actions opposite to those of urea a...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.96.11.6517

    authors: Burg MB,Peters EM,Bohren KM,Gabbay KH

    更新日期:1999-05-25 00:00:00

  • Fusion activation by a headless parainfluenza virus 5 hemagglutinin-neuraminidase stalk suggests a modular mechanism for triggering.

    abstract::The Paramyxoviridae family of enveloped viruses enters cells through the concerted action of two viral glycoproteins. The receptor-binding protein, hemagglutinin-neuraminidase (HN), H, or G, binds its cellular receptor and activates the fusion protein, F, which, through an extensive refolding event, brings viral and c...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1213813109

    authors: Bose S,Zokarkar A,Welch BD,Leser GP,Jardetzky TS,Lamb RA

    更新日期:2012-09-25 00:00:00

  • Regulation of the GABA cell phenotype in hippocampus of schizophrenics and bipolars.

    abstract::GABAergic dysfunction is present in the hippocampus in schizophrenia (SZ) and bipolar disorder (BD). The trisynaptic pathway was "deconstructed" into various layers of sectors CA3/2 and CA1 and gene expression profiling performed. Network association analysis was used to uncover genes that may be related to regulation...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0703806104

    authors: Benes FM,Lim B,Matzilevich D,Walsh JP,Subburaju S,Minns M

    更新日期:2007-06-12 00:00:00

  • Noradrenergic blockade stabilizes prefrontal activity and enables fear extinction under stress.

    abstract::Stress-induced impairments in extinction learning are believed to sustain posttraumatic stress disorder (PTSD). Noradrenergic signaling may contribute to extinction impairments by modulating medial prefrontal cortex (mPFC) circuits involved in fear regulation. Here we demonstrate that aversive fear conditioning rapidl...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1500682112

    authors: Fitzgerald PJ,Giustino TF,Seemann JR,Maren S

    更新日期:2015-07-14 00:00:00

  • Glutathione disulfide-stimulated Mg2+-ATPase of human erythrocyte membranes.

    abstract::Inside-out erythrocyte membranes attached to polycationic beads manifested glutathione disulfide (GSSG)-stimulated ATPase activity. A Lineweaver-Burk plot of the ATPase activity as a function of GSSG concentration was biphasic and gave apparent Km values of 0.13 mM and 2.0 mM. These kinetics are similar to those repor...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.84.21.7373

    authors: Kondo T,Kawakami Y,Taniguchi N,Beutler E

    更新日期:1987-11-01 00:00:00

  • Handoff from recombinase to replisome: insights from transposition.

    abstract::Bacteriophage Mu replicates as a transposable element, exploiting host enzymes to promote initiation of DNA synthesis. The phage-encoded transposase MuA, assembled into an oligomeric transpososome, promotes transfer of Mu ends to target DNA, creating a fork at each end, and then remains tightly bound to both forks. In...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章,评审

    doi:10.1073/pnas.111007898

    authors: Nakai H,Doseeva V,Jones JM

    更新日期:2001-07-17 00:00:00

  • Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations.

    abstract::We describe and test a Markov chain model of microsatellite evolution that can explain the different distributions of microsatellite lengths across different organisms and repeat motifs. Two key features of this model are the dependence of mutation rates on microsatellite length and a mutation process that includes bo...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.95.18.10774

    authors: Kruglyak S,Durrett RT,Schug MD,Aquadro CF

    更新日期:1998-09-01 00:00:00

  • An alternative pathway for rod signals in the rodent retina: rod photoreceptors, cone bipolar cells, and the localization of glutamate receptors.

    abstract::In the mammalian retina, extensive processing of spatiotemporal and chromatic information occurs. One key principle in signal transfer through the retina is parallel processing. Two of these parallel pathways are the ON- and OFF-channels transmitting light and dark signals. This dual system is created in the outer ple...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.96.24.14130

    authors: Hack I,Peichl L,Brandstätter JH

    更新日期:1999-11-23 00:00:00

  • Electrophoretic resolution of three major insulin receptor structures with unique subunit stoichiometries.

    abstract::Plasma membrane insulin receptors, affinity labeled by covalent crosslinking to receptor-bound 125I-labeled insulin, are shown to appear as a heterogeneous population of three major disulfide-linked complexes (Mr 350,000, 320,000, and 290,000) upon electrophoresis in highly porous dodecyl sulfate/polyacrylamide gels i...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.77.12.7137

    authors: Massague J,Pilch PF,Czech MP

    更新日期:1980-12-01 00:00:00

  • Enteroendocrine precursors differentiate independently of Wnt and form serotonin expressing adenomas in response to active beta-catenin.

    abstract::Wnt signaling is required for the maintenance of intestinal stem cells and self-renewal of the intestinal epithelium. Intestinal cancers are frequently associated with mutations that activate the Wnt pathway. The role of Wnt signaling on differentiation of lineage-specific precursors in the intestine is not well chara...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0702665104

    authors: Wang Y,Giel-Moloney M,Rindi G,Leiter AB

    更新日期:2007-07-03 00:00:00

  • Association of the adenovirus DNA-binding protein with RNA both in vitro and in vivo.

    abstract::The multifunctional DNA-binding protein (DBP) encoded by human adenovirus binds RNA. The association of purified DBP with RNA in vitro was demonstrated by using either a gel filtration or a filter binding assay. This association is sensitive to ionic strength and exhibits no apparent sequence specificity. DBP also int...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.83.23.8947

    authors: Cleghon VG,Klessig DF

    更新日期:1986-12-01 00:00:00

  • Water does not flow across the tight junctions of MDCK cell epithelium.

    abstract::Although it has been known for decades that the tight junctions of fluid-transporting epithelia are leaky to ions, it has not been possible to determine directly whether significant transjunctional water movement also occurs. An optical microscopic technique was developed for the direct visualization of the flow veloc...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.95.11.6526

    authors: Kovbasnjuk O,Leader JP,Weinstein AM,Spring KR

    更新日期:1998-05-26 00:00:00

  • A neurohistochemical blueprint for pain-induced loss of appetite.

    abstract::A common complaint among pain patients is that they lose their appetite. These accounts are anecdotal, however, and the neural mechanism underlying pain-induced loss of appetite remains unknown. In this study, we documented the occurrence of appetite loss in patients under migraine attack and investigated the neuronal...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.171616898

    authors: Malick A,Jakubowski M,Elmquist JK,Saper CB,Burstein R

    更新日期:2001-08-14 00:00:00

  • Identification of tissue-specific cell death using methylation patterns of circulating DNA.

    abstract::Minimally invasive detection of cell death could prove an invaluable resource in many physiologic and pathologic situations. Cell-free circulating DNA (cfDNA) released from dying cells is emerging as a diagnostic tool for monitoring cancer dynamics and graft failure. However, existing methods rely on differences in DN...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1519286113

    authors: Lehmann-Werman R,Neiman D,Zemmour H,Moss J,Magenheim J,Vaknin-Dembinsky A,Rubertsson S,Nellgård B,Blennow K,Zetterberg H,Spalding K,Haller MJ,Wasserfall CH,Schatz DA,Greenbaum CJ,Dorrell C,Grompe M,Zick A,Hubert A,M

    更新日期:2016-03-29 00:00:00