Substrate specificity of the DNA unwinding activity of the RecBC enzyme of Escherichia coli.

Abstract:

:The RecBC enzyme of Escherichia coli promotes genetic recombination of phage or bacterial chromosomes. The purified enzyme travels through duplex DNA, unwinding and rewinding the DNA with the transient production of potentially recombinogenic single-stranded DNA. The studies reported here are aimed at understanding which chromosomal forms allow the entry of RecBC enzyme and hence may undergo RecBC enzyme-mediated recombination. Circular duplex molecules, whether covalently closed, nicked or containing single-stranded gaps of 10 to 774 nucleotides, are not detectably unwound by RecBC enzyme. Linear duplex molecules are readily unwound if they have a nearly flush-ended terminus whose 5' and 3' ends are offset by no more than about 25 nucleotides; molecules with longer single-stranded tails are poorly bound by RecBC enzyme and are infrequently unwound. The single-strand endonuclease activity of RecBC enzyme can slowly cleave gapped circles to produce molecules presumably capable of being unwound. These results provide an enzymatic basis for the recombinogenicity of double-stranded DNA ends established from genetic studies of RecBC enzyme and Chi sites, recognition sites for RecBC enzyme-mediated DNA strand cleavage.

journal_name

J Mol Biol

authors

Taylor AF,Smith GR

doi

10.1016/0022-2836(85)90414-0

subject

Has Abstract

pub_date

1985-09-20 00:00:00

pages

431-43

issue

2

eissn

0022-2836

issn

1089-8638

pii

0022-2836(85)90414-0

journal_volume

185

pub_type

杂志文章
  • Mediator Architecture and RNA Polymerase II Interaction.

    abstract::Integrated structural biology recently elucidated the architecture of Mediator and its position on RNA polymerase II. Here we summarize these achievements and list open questions on Mediator structure and mechanism. ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2016.01.028

    authors: Plaschka C,Nozawa K,Cramer P

    更新日期:2016-06-19 00:00:00

  • RNA binding, packaging and polymerase activities of the different incomplete polymerase complex particles of dsRNA bacteriophage phi 6.

    abstract::phi 6 is an enveloped dsRNA bacterial virus. Its segmented genome resides inside the virion associated polymerase complex which is formed by four proteins (P1, P2, P4 and P7) encoded by the viral L segment. Complete and incomplete polymerase complex particles can be produced using cDNA copies of this largest genome se...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0317

    authors: Juuti JT,Bamford DH

    更新日期:1995-06-09 00:00:00

  • An on-pathway hidden intermediate and the early rate-limiting transition state of Rd-apocytochrome b562 characterized by protein engineering.

    abstract::The folding pathway of Rd-apocytochrome b562, a four-helix bundle protein, was characterized using Trp and Ala/Gly pair mutations. We found that the Trp mutants (F65W) of both the fully folded Rd-apocytochrome b562 and a partially unfolded intermediate with the N-terminal helix (helix I) unfolded, fold with identical ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.07.057

    authors: Zhou Z,Huang Y,Bai Y

    更新日期:2005-09-30 00:00:00

  • Functional analysis of human tRNA isodecoders.

    abstract::tRNA isodecoders share the same anticodon but have differences in their body sequence. An unexpected result from genome sequencing projects is the identification of a large number of tRNA isodecoder genes in mammalian genomes. In the reference human genome, more than 270 isodecoder genes are present among the approxim...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.12.018

    authors: Geslain R,Pan T

    更新日期:2010-02-26 00:00:00

  • Interleukin 35 Regulatory B Cells.

    abstract::B lymphocytes play a central role in host immunity. They orchestrate humoral immune responses that modulate activities of other immune cells and produce neutralizing antibodies that confer lasting immunity to infectious diseases including smallpox, measles and poliomyelitis. In addition to these traditional functions ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2020.07.019

    authors: Choi JK,Egwuagu CE

    更新日期:2021-01-08 00:00:00

  • Internal promoter elements of transfer RNA genes are preferentially exposed in chromatin.

    abstract::We have examined the chromatin organization of a cluster of transfer RNA genes at the cytogenic locus 90BC on the right arm of the third Drosophila melanogaster chromosome. We find that the internal promoter sequences are preferentially exposed to micrococcal nuclease and DNase I in chromatin. Moreover, these exposed ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(84)90158-x

    authors: DeLotto R,Schedl P

    更新日期:1984-11-15 00:00:00

  • Crystallization of and preliminary X-ray data for the mouse major urinary protein and rat alpha-2u globulin.

    abstract::Crystals of the mouse major urinary protein (MUP) and rat alpha-2u globulin (AMG) have been grown from solutions of polyethylene glycol 3350 and CdCl2, respectively. The crystals differ both in their morphologies and space groups but have very similar unit cell sizes. AMG crystallized in P2(1) (a = 56.6 A, b = 103.8 A...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(91)90258-8

    authors: Böcskei Z,Findlay JB,North AC,Phillips SE,Somers WS,Wright CE,Lionetti C,Tirindelli R,Cavaggioni A

    更新日期:1991-04-20 00:00:00

  • The Rhodobacter sphaeroides ECF sigma factor, sigma(E), and the target promoters cycA P3 and rpoE P1.

    abstract::Rhodobacter sphaeroides rpoE encodes a 19.2 kDa protein, sigma(E), related to members of the extra-cytoplasmic function subfamily of eubacterial RNA polymerase sigma factors. We demonstrate that sigma(E) directs transcription from rpoE P1, the promoter for the rpoEchrR operon, and from cycA P3, a promoter for the cyto...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3263

    authors: Newman JD,Falkowski MJ,Schilke BA,Anthony LC,Donohue TJ

    更新日期:1999-11-26 00:00:00

  • Conservation of transition state structure in fast folding peripheral subunit-binding domains.

    abstract::Phi-value analysis was used to characterise the structure of the transition state (TS) for folding of POB L146A Y166W, a peripheral subunit-binding domain that folds in microseconds. Helix 2 was structured in the TS with consolidating interactions from the structured loop that connects the two alpha-helices. This dist...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.06.081

    authors: Sharpe TD,Ferguson N,Johnson CM,Fersht AR

    更新日期:2008-10-31 00:00:00

  • Functionally important correlated motions in the single-stranded DNA-binding protein encoded by filamentous phage Pf3.

    abstract::To elucidate the interplay between different parts of dimeric single-stranded DNA-binding proteins we have studied the correlated motions in the protein encoded by filamentous phage Pf3 via the combined use of 15N-NMR relaxation experiments, molecular dynamics simulations and essential dynamics calculations. These stu...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2629

    authors: Horstink LM,Abseher R,Nilges M,Hilbers CW

    更新日期:1999-04-02 00:00:00

  • Genomic organization and physical mapping of the transfer RNA genes in Escherichia coli K12.

    abstract::By using a set of 476 ordered DNA clones (in lambda phage vector) that covers the entire chromosome of Escherichia coli K12, we have made an exhaustive survey of tRNA genes in the E. coli genome. Ultraviolet-irradiated bacteria were separately infected with each of the 476 clones and the RNA molecules produced upon in...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(90)90224-A

    authors: Komine Y,Adachi T,Inokuchi H,Ozeki H

    更新日期:1990-04-20 00:00:00

  • Advances in Understanding Stimulus-Responsive Phase Behavior of Intrinsically Disordered Protein Polymers.

    abstract::Proteins and synthetic polymers can undergo phase transitions in response to changes to intensive solution parameters such as temperature, proton chemical potentials (pH), and hydrostatic pressure. For proteins and protein-based polymers, the information required for stimulus-responsive phase transitions is encoded in...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2018.06.031

    authors: Ruff KM,Roberts S,Chilkoti A,Pappu RV

    更新日期:2018-11-02 00:00:00

  • Immunoglobulin G1 Fc domain motions: implications for Fc engineering.

    abstract::The fragment crystallizable (Fc) region links the key pathogen identification and destruction properties of immunoglobulin G (IgG). Pathogen opsonization positions Fcs to activate pro-inflammatory Fcγ receptors (FcγRs) on immune cells. The cellular response and committal to a damaging, though protective, immune respon...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2014.01.011

    authors: Frank M,Walker RC,Lanzilotta WN,Prestegard JH,Barb AW

    更新日期:2014-04-17 00:00:00

  • Aminoglycoside resistance by ArmA-mediated ribosomal 16S methylation in human bacterial pathogens.

    abstract::Aminoglycosides are a medically important class of antibiotics used to treat serious infections. Methylation of the ribosomal target is an emerging mechanism that produces a high level of resistance to all clinically available aminoglycosides for systemic therapy except streptomycin. ArmA was the first methyltransfera...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.03.038

    authors: Liou GF,Yoshizawa S,Courvalin P,Galimand M

    更新日期:2006-06-02 00:00:00

  • Effects of cobalt hexammine on folding and self-cleavage of the Neurospora VS ribozyme.

    abstract::We have investigated the effects of Co(NH3)6(3+), an analog of hexahydrated Mg2+, on folding and catalysis of the Neurospora VS ribozyme. Most of the metal ion-induced changes detected by chemical modification structure probing in either metal ion are similar, but occur at approximately 33-fold lower concentrations of...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2001.4625

    authors: Maguire JL,Collins RA

    更新日期:2001-05-25 00:00:00

  • A second pathway to degrade pyrimidine nucleic acid precursors in eukaryotes.

    abstract::Pyrimidine bases are the central precursors for RNA and DNA, and their intracellular pools are determined by de novo, salvage and catabolic pathways. In eukaryotes, degradation of uracil has been believed to proceed only via the reduction to dihydrouracil. Using a yeast model, Saccharomyces kluyveri, we show that duri...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.05.029

    authors: Andersen G,Björnberg O,Polakova S,Pynyaha Y,Rasmussen A,Møller K,Hofer A,Moritz T,Sandrini MP,Merico AM,Compagno C,Akerlund HE,Gojković Z,Piskur J

    更新日期:2008-07-18 00:00:00

  • NMR structure of the amino-terminal domain of the lambda integrase protein in complex with DNA: immobilization of a flexible tail facilitates beta-sheet recognition of the major groove.

    abstract::The integrase protein (Int) from bacteriophage lambda is the archetypal member of the tyrosine recombinase family, a large group of enzymes that rearrange DNA in all domains of life. Int catalyzes the insertion and excision of the viral genome into and out of the Escherichia coli chromosome. Recombination transpires w...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.03.041

    authors: Fadeev EA,Sam MD,Clubb RT

    更新日期:2009-05-15 00:00:00

  • Crystallization and preliminary X-ray study of a recombinant cutinase from Fusarium solani pisi.

    abstract::Recombinant cutinase from Fusarium solani pisi is expressed and excreted with very high yields in Escherichia coli cultures. Cutinase was crystallized at 20 degrees C using the vapour diffusion technique, with polyethylene glycol 6000 as precipitant. Best crystals were obtained at pH 7.0 with polyethylene glycol 6000 ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/S0022-2836(05)80339-0

    authors: Abergel C,Martinez C,Fontecilla-Camps J,Cambillau C,de Geus P,Lauwereys M

    更新日期:1990-09-20 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

  • Catalysis by Glomerella cingulata cutinase requires conformational cycling between the active and inactive states of its catalytic triad.

    abstract::Cutinase belongs to a group of enzymes that catalyze the hydrolysis of esters and triglycerides. Structural studies on the enzyme from Fusarium solani have revealed the presence of a classic catalytic triad that has been implicated in the enzyme's mechanism. We have solved the crystal structure of Glomerella cingulata...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.10.050

    authors: Nyon MP,Rice DW,Berrisford JM,Hounslow AM,Moir AJ,Huang H,Nathan S,Mahadi NM,Bakar FD,Craven CJ

    更新日期:2009-01-09 00:00:00

  • Predictive QM/MM Modeling of Modulations in Protein-Protein Binding by Lysine Methylation.

    abstract::Lysine methylation is a key regulator of protein-protein binding. The amine group of lysine can accept up to three methyl groups, and experiments show that protein-protein binding free energies are sensitive to the extent of methylation. These sensitivities have been rationalized in terms of chemical and structural fe...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2020.166745

    authors: Rahman S,Wineman-Fisher V,Al-Hamdani Y,Tkatchenko A,Varma S

    更新日期:2021-02-05 00:00:00

  • Purification and crystallization of fumarase C from Escherichia coli.

    abstract::Fumarase C purified from Escherichia coli has been crystallized in the presence of polyethylene glycol in both a citrate buffer at pH 5.3 and a 3-(4-morpholino)-propanesulfonic acid buffer at pH 7.5 yielding two crystal forms. An orthorhombic C222(1) form was obtained in citrate at pH 5.3 and an orthorhombic I222 form...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1993.1264

    authors: Weaver TM,Levitt DG,Banaszak LJ

    更新日期:1993-05-05 00:00:00

  • The oligomeric structure of vaccinia viral envelope protein A27L is essential for binding to heparin and heparan sulfates on cell surfaces: a structural and functional approach using site-specific mutagenesis.

    abstract::The soluble domain of the self-assembly vaccinia virus envelope protein A27L, sA27L-aa, consists of a flexible extended coil at the N terminus and a rigid hydrophobic coiled-coil region at the C terminus. In the former, a basic strip of 12 residues is responsible for binding to cell-surface heparan sulfates. Although ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.04.024

    authors: Ho Y,Hsiao JC,Yang MH,Chung CS,Peng YC,Lin TH,Chang W,Tzou DL

    更新日期:2005-06-24 00:00:00

  • Engineering activity and stability of Thermotoga maritima glutamate dehydrogenase. II: construction of a 16-residue ion-pair network at the subunit interface.

    abstract::The role of an 18-residue ion-pair network, that is present in the glutamate dehydrogenase from the hyperthermophilic archaeon Pyrococcus furiosus, in conferring stability to other, less stable homologous enzymes, has been studied by introducing four new charged amino acid residues into the subunit interface of glutam...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2779

    authors: Lebbink JH,Knapp S,van der Oost J,Rice D,Ladenstein R,de Vos WM

    更新日期:1999-06-04 00:00:00

  • Direct selection of antibodies from complex libraries with the protein fragment complementation assay.

    abstract::The aim of the present study was to develop the protein fragment complementation assay (PCA) for the intracellular selection of specific binding molecules from the fully synthetic HuCAL antibody library. Here, we describe the first successful selections of specific antibodies by PCA, and we discuss the opportunities a...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.12.043

    authors: Koch H,Gräfe N,Schiess R,Plückthun A

    更新日期:2006-03-24 00:00:00

  • Visualization of the unwinding of long DNA chains by the herpes simplex virus type 1 UL9 protein and ICP8.

    abstract::UL9 protein and ICP8 encoded by the herpes simplex virus type 1 (HSV-1) were shown to catalyze a highly active, non-origin-dependent unwinding of DNA. UL9 protein, the HSV-1 origin binding protein, as a modest helicase activity that is greatly stimulated by the HSV-1 single strand (ss) binding protein, ICP8. Here, ele...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1996.0287

    authors: Makhov AM,Boehmer PE,Lehman IR,Griffith JD

    更新日期:1996-05-24 00:00:00

  • Minimum-energy path for a u6 RNA conformational change involving protonation, base-pair rearrangement and base flipping.

    abstract::The U6 RNA internal stem-loop (U6 ISL) is a highly conserved domain of the spliceosome that is important for pre-mRNA splicing. The U6 ISL contains an internal loop that is in equilibrium between two conformations controlled by the protonation state of an adenine (pK(a)=6.5). Lower pH favors formation of a protonated ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2009.07.003

    authors: Venditti V,Clos L 2nd,Niccolai N,Butcher SE

    更新日期:2009-09-04 00:00:00

  • The 3'-tail of a forked-duplex sterically determines whether one or two DNA strands pass through the central channel of a replication-fork helicase.

    abstract::DnaB helicase is a ring-shaped hexamer that unwinds DNA at a replication fork. To understand how this protein interacts with DNA during unwinding, DnaB from Thermus aquaticus was incubated with chemically modified forked-duplex DNA substrates and the unwinding rates were measured. Unwinding was inhibited by modificati...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3965

    authors: Kaplan DL

    更新日期:2000-08-11 00:00:00

  • The Helicobacter pylori CagD (HP0545, Cag24) protein is essential for CagA translocation and maximal induction of interleukin-8 secretion.

    abstract::Pathogenic strains of Helicobacter pylori use a type IV secretion system (T4SS) to deliver the toxin CagA into human host cells. The T4SS, along with the toxin itself, is coded into a genomic insert, which is termed the cag pathogenicity island. The cag pathogenicity island contains about 30 open-reading frames, for m...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.12.018

    authors: Cendron L,Couturier M,Angelini A,Barison N,Stein M,Zanotti G

    更新日期:2009-02-13 00:00:00

  • Differential expression of two clusters of mouse histone genes.

    abstract::The mouse histone mRNAs coded for by three different cloned DNA fragments have been characterized. Two of these cloned DNA fragments, MM221 and MM291, located on chromosome 13, code for H3, H2b and H2a histone mRNAs, which are expressed at low levels in cultured mouse cells and fetal mice. The other DNA fragment, MM61...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(85)90211-6

    authors: Graves RA,Wellman SE,Chiu IM,Marzluff WF

    更新日期:1985-05-25 00:00:00