当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > Core RNA polymerase and promoter DNA interactions of purified domains of sigma N: bipartite functions.

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, respectively. The NH2-terminal Region I is required for the correct interaction of holoenzyme with the promoter, and promoter complexes forming with a truncated sigma N lacking Region I are not activatable. The complexes lack the DNA structure believed to represent nucleated strand separation but still make close contacts with this promoter part. Determinants of specific DNA recognition by sigma N were shown to reside in a C-terminal 16 kDa peptide, and core RNA polymerase binding determinants in an adjacent peptide. The latter contacts and appears to pack against the DNA-binding domain. Thus the DNA-binding and core-binding domains are bipartite in function, consistent with core functioning as an allosteric effector of the sigma DNA-binding activity. The DNA-binding and core-binding domains together include Region III of sigma N. Although not the primary determinant of core or DNA recognition, the acidic Region II of sigma N influenced both activities. Regions I and II in combination with core RNA polymerase thus appear to control the activity of C-terminal DNA contacting surfaces to allow formation of a closed promoter complex that is susceptible to activation.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

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

doi

10.1006/jmbi.1995.0260

subject

Has Abstract

pub_date

1995-05-12 00:00:00

pages

781-803

issue

4

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(85)70260-4

journal_volume

248

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Early events in murine erythroleukemia cells induced to differentiate. Accumulation and gene expression of the transformation-associated cellular protein p53.

    abstract：:Oncogenes may play a crucial role in the genetic program of cellular differentiation; even, probably, at a very early stage in this program, which can be described as pre-commitment. We have investigated the variation in, and the control level of, the accumulation of the transformation-associated cellular protein p53 ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(88)90333-6

    authors： Khochbin S,Principaud E,Chabanas A,Lawrence JJ

    更新日期：1988-03-05 00:00:00

  • Crystallization of a new form of the eye lens protein beta B2-crystallin.

    abstract：:A new crystal form of the bovine oligomeric lens protein beta B2 has been grown in the presence of calcium acetate. The crystals are orthorhombic, I222 or I2(1)2(1)2(1), with cell dimensions a = 77.8 A, b = 83.6 A, c = 109.2 A. This new crystal form, which diffracts to at least 2.5 A, has a and b cell dimensions that ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(89)90162-9

    authors： Bax B,Slingsby C

    更新日期：1989-08-20 00:00:00

  • Structural, biochemical, and in vivo characterization of the first virally encoded cyclophilin from the Mimivirus.

    abstract：:Although multiple viruses utilize host cell cyclophilins, including severe acute respiratory syndrome (SARS) and human immunodeficiency virus type-1(HIV-1), their role in infection is poorly understood. To help elucidate these roles, we have characterized the first virally encoded cyclophilin (mimicyp) derived from th...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.08.051

    authors： Thai V,Renesto P,Fowler CA,Brown DJ,Davis T,Gu W,Pollock DD,Kern D,Raoult D,Eisenmesser EZ

    更新日期：2008-04-18 00:00:00

  • Thermus thermophilus cytochrome-c552: A new highly thermostable cytochrome-c structure obtained by MAD phasing.

    abstract：:The three-dimensional structure of cytochrome-c552 from Thermus thermophilus has been determined by the multiple anomalous dispersion technique using synchrotron radiation and refined to a resolution of 1.28 A. Data collection at 90 K and the recording of three data sets (f'-minimum: 7125 eV, f"-maximum: 7138 eV and r...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1997.1181

    authors： Than ME,Hof P,Huber R,Bourenkov GP,Bartunik HD,Buse G,Soulimane T

    更新日期：1997-08-29 00:00:00

  • Phospholipids in Autophagosome Formation and Fusion.

    abstract：:Autophagosomes are double membrane organelles that are formed during a process referred to as macroautophagy. They serve to deliver cytoplasmic material into the lysosome for degradation. Autophagosomes are formed in a de novo manner and are the result of substantial membrane remodeling processes involving numerous pr...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2016.10.029

    authors： Martens S,Nakamura S,Yoshimori T

    更新日期：2016-10-27 00:00:00

  • Multimodal and Polymorphic Interactions between Anillin and Actin: Their Implications for Cytokinesis.

    abstract：:Cytokinesis of animal cells requires the assembly of a contractile ring, which promotes daughter cell splitting. Anillin is a conserved scaffold protein involved in organizing the structural components of the contractile ring including filamentous actin (F-actin), myosin, and septins and in forming the subsequent midb...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2017.01.020

    authors： Jananji S,Risi C,Lindamulage IKS,Picard LP,Van Sciver R,Laflamme G,Albaghjati A,Hickson GRX,Kwok BH,Galkin VE

    更新日期：2017-03-10 00:00:00

  • Self-interaction of pneumolysin, the pore-forming protein toxin of Streptococcus pneumoniae.

    abstract：:The pathogenically important cholesterol-binding pore-forming bacterial "thiol-activated" toxins (TATs) are commonly believed to be monomeric in solution and to undergo a transition on membrane binding mediated by cholesterol to an oligomeric pore. We present evidence, gained through the application of a number of bio...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2258

    authors： Gilbert RJ,Rossjohn J,Parker MW,Tweten RK,Morgan PJ,Mitchell TJ,Errington N,Rowe AJ,Andrew PW,Byron O

    更新日期：1998-12-11 00:00:00

  • The crystal structure of the trigonal decamer C-G-A-T-C-G-6meA-T-C-G: a B-DNA helix with 10.6 base-pairs per turn.

    abstract：:The B-DNA decanucleotide C-G-A-T-C-G-6meA-T-C-G has been crystallized under the same conditions used earlier for C-G-A-T-C-G-A-T-C-G, but is found to adopt a new trigonal P3(2)21 packing mode instead of the expected orthorhombic P2(1)2(1)2(1) form. Unit cell dimensions a = b = 33.38 A, c = 98.30 A, gamma = 120 degrees...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1325

    authors： Baikalov I,Grzeskowiak K,Yanagi K,Quintana J,Dickerson RE

    更新日期：1993-06-05 00:00:00

  • Zooming in on the hydrophobic ridge of H-2D(b): implications for the conformational variability of bound peptides.

    abstract：:Class I major histocompatibility complex (MHC) molecules, which display intracellularly processed peptides on the cell surface for scanning by T-cell receptors (TCRs), are extraordinarily polymorphic. MHC polymorphism is believed to result from natural selection, since individuals heterozygous at the corresponding loc...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.5016

    authors： Ciatto C,Tissot AC,Tschopp M,Capitani G,Pecorari F,Plückthun A,Grütter MG

    更新日期：2001-10-05 00:00:00

  • Discovery and Function of B-Cell IgD Low (BDL) B Cells in Immune Tolerance.

    abstract：:It is now appreciated that in addition to their role in humoral immunity, B cells also exert regulatory mechanisms that lead to attenuation of inflammatory responses. The concept of B-cell regulation became well recognized when mice deficient in B cells due to genetic disruption were shown to be refractory to recovery...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章,评审

    doi：10.1016/j.jmb.2020.06.023

    authors： Khalil MI,Gurski CJ,Dittel LJ,Neu SD,Dittel BN

    更新日期：2021-01-08 00:00:00

  • A generic mechanism of beta2-microglobulin amyloid assembly at neutral pH involving a specific proline switch.

    abstract：:Although numerous measurements of amyloid assembly of different proteins under distinct conditions in vitro have been performed, the molecular mechanisms underlying the specific self-association of proteins into amyloid fibrils remain obscure. Elucidating the nature of the events that initiate amyloid formation remain...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.01.013

    authors： Eichner T,Radford SE

    更新日期：2009-03-13 00:00:00

  • Protein-protein Förster resonance energy transfer analysis of nucleosome core particles containing H2A and H2A.Z.

    abstract：:A protein-protein Förster resonance energy transfer (FRET) system, employing probes at multiple positions, was designed to specifically monitor the dissociation of the H2A-H2B dimer from the nucleosome core particle (NCP). Tryptophan donors and Cys-AEDANS acceptors were chosen because, compared to previous NCP FRET fl...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.05.075

    authors： Hoch DA,Stratton JJ,Gloss LM

    更新日期：2007-08-24 00:00:00

  • Molecular insights into the interaction between alpha-synuclein and docosahexaenoic acid.

    abstract：:alpha-Synuclein (alpha-syn) is a 140-residue protein of unknown function, involved in several neurodegenerative disorders, such as Parkinson's disease. Recently, the possible interaction between alpha-syn and polyunsaturated fatty acids has attracted a strong interest. Indeed, lipids are able to trigger the multimeriz...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.09.008

    authors： De Franceschi G,Frare E,Bubacco L,Mammi S,Fontana A,de Laureto PP

    更新日期：2009-11-20 00:00:00

  • Effect of pseudorepeat rearrangement on alpha-synuclein misfolding, vesicle binding, and micelle binding.

    abstract：:The pathological and physiological hallmarks of the protein alpha-synuclein (aS) are its misfolding into cytotoxic aggregates and its binding to synaptic vesicles, respectively. Both events are mediated by seven 11-residue amphiphilic pseudorepeats and, most generally, involve a transition from intrinsically unstructu...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.05.058

    authors： Rao JN,Kim YE,Park LS,Ulmer TS

    更新日期：2009-07-17 00:00:00

  • Stopped-flow kinetic analysis of the interaction of Escherichia coli RNA polymerase with the bacteriophage T7 A1 promoter.

    abstract：:We have conducted a detailed kinetic and thermodynamic analysis of open complex formation between Escherichia coli RNA polymerase and the A1 promoter from bacteriophage T7 by monitoring alterations in the intrinsic protein fluorescence of RNA polymerase in stopped-flow kinetic studies. The stopped-flow kinetic data ar...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2101

    authors： Johnson RS,Chester RE

    更新日期：1998-10-23 00:00:00

  • Active site trapping of nucleotide by smooth and non-muscle myosins.

    abstract：:The folded 10 S monomer conformation of smooth muscle myosin traps the hydrolysis products ADP and Pi in its active sites. To test the significance of this, we have searched for equivalent trapping in other conformational and assembly states of avian gizzard and brush border myosins, using formycin triphosphate (FTP) ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(88)90100-3

    authors： Cross RA,Jackson AP,Citi S,Kendrick-Jones J,Bagshaw CR

    更新日期：1988-09-05 00:00:00

  • Structural polymorphism of Methanothermobacter thermautotrophicus MCM.

    abstract：:The minichromosome maintenance (MCM) proteins are essential for replication initiation and elongation in eukarya and archaea. There are six MCM proteins in eukaryotes, and MCM complexes are believed to unwind DNA during chromosomal DNA replication. However, the mechanism and structure of the MCM complexes are not know...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.11.076

    authors： Chen YJ,Yu X,Kasiviswanathan R,Shin JH,Kelman Z,Egelman EH

    更新日期：2005-02-18 00:00:00

  • Monitoring Ligand-Induced Protein Ordering in Drug Discovery.

    abstract：:While the gene for p53 is mutated in many human cancers causing loss of function, many others maintain a wild-type gene but exhibit reduced p53 tumor suppressor activity through overexpression of the negative regulators, Mdm2 and/or MdmX. For the latter mechanism of loss of function, the activity of endogenous p53 can...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2016.01.016

    authors： Grace CR,Ban D,Min J,Mayasundari A,Min L,Finch KE,Griffiths L,Bharatham N,Bashford D,Kiplin Guy R,Dyer MA,Kriwacki RW

    更新日期：2016-03-27 00:00:00

  • Repressor assembly at trp binding sites is dependent on the identity of the intervening dinucleotide between the binding half sites.

    abstract：:The interaction of trp repressor with its DNA targets is unusual in that specific recognition in this system does not rely exclusively on direct hydrogen bonds to the DNA bases that are crucial for sequence-specific recognition. It has been suggested that trp operators are mainly recognized by water-mediated interacti...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0826

    authors： Bareket-Samish A,Cohen I,Haran TE

    更新日期：1997-03-21 00:00:00

  • Fragment ranking in modelling of protein structure. Conformationally constrained environmental amino acid substitution tables.

    abstract：:Conformationally constrained environment-dependent amino acid residue substitution tables have been constructed from a database comprising 33 homologous families of protein sequences aligned on the basis of their three-dimensional structures. Residues are allotted to one of 216 (or 54) classes of combinations of struc...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1018

    authors： Topham CM,McLeod A,Eisenmenger F,Overington JP,Johnson MS,Blundell TL

    更新日期：1993-01-05 00:00:00

  • Structure and fluctuations of bacteriorhodopsin in the purple membrane: a molecular dynamics study.

    abstract：:Molecular dynamics simulations on bacteriorhodopsin were performed starting from the model structure described by Henderson et al. The simulations were gradually improved by first treating a monomer in vacuum and then adding further monomers, lipids, and water to finally simulate a unit cell of the hexagonal lattice o...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1995.0361

    authors： Edholm O,Berger O,Jähnig F

    更新日期：1995-06-30 00:00:00

  • Crystallization and preliminary X-ray analysis of Gc, the vitamin D-binding protein in serum.

    abstract：:The vitamin D-binding protein, Gc, was purified from human serum and crystallized using the hanging-drop method. The best crystals were grown from 28% polyethylene glycol 400 in 50 mM-sodium acetate at pH 4.8. These crystals diffract to 3.4 A and the observed diffraction is consistent with orthorhombic space groups P4...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(91)90097-p

    authors： Vogelaar NJ,Lindberg U,Schutt CE

    更新日期：1991-08-05 00:00:00

  • V-shaped scaffold: a new architectural motif identified in an A x (G x G x G x G) pentad-containing dimeric DNA quadruplex involving stacked G(anti) x G(anti) x G(anti) x G(syn) tetrads.

    abstract：:We report the results of an NMR study of unlabeled and uniformly (13)C,(15)N-labeled d(G(3)AG(2)T(3)G(3)AT) in 100 mM NaCl, conditions under which it forms a dimeric quadruplex containing several new topological features. The DNA oligomer chain in each symmetry-related monomer subunit undergoes three sharp turns to fo...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.2001.4916

    authors： Zhang N,Gorin A,Majumdar A,Kettani A,Chernichenko N,Skripkin E,Patel DJ

    更新日期：2001-08-31 00:00:00

  • Modelling transcriptional interference and DNA looping in gene regulation.

    abstract：:We describe a hybrid statistical mechanical and dynamical approach for modelling the formation of closed, open and elongating complexes of RNA polymerase, the interactions of these polymerases to produce transcriptional interference, and the regulation of these processes by a DNA-binding and DNA-looping regulatory pro...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.04.041

    authors： Dodd IB,Shearwin KE,Sneppen K

    更新日期：2007-06-22 00:00:00

  • Bile acid interactions with rabbit ileal lipid binding protein and an engineered helixless variant reveal novel ligand binding properties of a versatile beta-clam shell protein scaffold.

    abstract：:The intracellular ileal lipid binding proteins (ILBPs) are involved in the transport and enterohepatic circulation of bile acids. ILBPs from different species show high sequence and structural homology and have been shown to bind multiple bile acid ligands with differing degrees of selectivity and positive co-operativ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.06.024

    authors： Kouvatsos N,Thurston V,Ball K,Oldham NJ,Thomas NR,Searle MS

    更新日期：2007-08-31 00:00:00

  • Plasticity within the obligatory folding nucleus of an immunoglobulin-like domain.

    abstract：:A number of beta-sandwich immunoglobulin-like domains have been shown to fold using a set of structurally equivalent residues that form a folding nucleus deep within the core of the protein. Formation of this nucleus is sufficient to establish the complex Greek key topology of the native state. These nucleating residu...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.09.088

    authors： Lappalainen I,Hurley MG,Clarke J

    更新日期：2008-01-11 00:00:00

  • Protein titration in the crystal state.

    abstract：:Proteins are complex structures whose overall stability critically depends on a delicate balance of numerous interactions of similar strength, which are markedly influenced by their environment. Here, we present an analysis of the effect of pH on a protein structure in the crystalline state using RNase A as a model sy...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.3093

    authors： Berisio R,Lamzin VS,Sica F,Wilson KS,Zagari A,Mazzarella L

    更新日期：1999-10-01 00:00:00

  • Dissecting specificity in the Janus kinases: the structures of JAK-specific inhibitors complexed to the JAK1 and JAK2 protein tyrosine kinase domains.

    abstract：:The Janus kinases (JAKs) are a pivotal family of protein tyrosine kinases (PTKs) that play prominent roles in numerous cytokine signaling pathways, with aberrant JAK activity associated with a variety of hematopoietic malignancies, cardiovascular diseases and immune-related disorders. Whereas the structures of the JAK...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.01.041

    authors： Williams NK,Bamert RS,Patel O,Wang C,Walden PM,Wilks AF,Fantino E,Rossjohn J,Lucet IS

    更新日期：2009-03-20 00:00:00

  • Proteolytic and conformational control of virus capsid maturation: the bacteriophage HK97 system.

    abstract：:Bacteriophage capsid assembly pathways provide excellent model systems to study large-scale conformational changes and other mechanisms that regulate the formation of macromolecular complexes. These capsids are formed from proheads: relatively fragile precursor particles which mature by undergoing extensive remodeling...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1995.0538

    authors： Conway JF,Duda RL,Cheng N,Hendrix RW,Steven AC

    更新日期：1995-10-13 00:00:00

  • Regulation of c-fos expression by RNA polymerase elongation competence.

    abstract：:The molecular mechanisms underlying transcription elongation and their role in gene regulation are poorly characterized in eukaryotes. A number of genes, however, have been proposed to be regulated at the level of transcription elongation, including c-myc, c-fos and c-myb. Here, we analyze the control of transcription...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.1905

    authors： Pinaud S,Mirkovitch J

    更新日期：1998-07-31 00:00:00