The RecB nuclease domain binds to RecA-DNA filaments: implications for filament loading.

Abstract:

:The E. coli RecBCD enzyme facilitates the loading of RecA onto single-stranded DNA produced by the combined helicase/nuclease activity of RecBCD. The nuclease domain of RecB protein, RecB(nuc), has been previously shown to bind RecA. Surprisingly, RecB(nuc) also binds to phage and eukaryotic homologs of RecA, leading to the suggestion that RecB(nuc) interacts with the polymerization motif that is present in all three proteins. This mode of interaction could only be with monomeric RecA, as this motif would be buried in filaments. We show that RecB(nuc) binds extensively to the outside of RecA-DNA filaments. Three-dimensional reconstructions suggest that RecB(nuc) binds to the ATP-binding core of RecA, with a displacement of the C-terminal domain of RecA. Solution experiments confirm that the interaction of RecB(nuc) is only with the RecA core. Since the RecA C-terminal domain has been shown to be regulatory, the interaction observed may be part of the loading mechanism where RecB displaces the RecA C-terminal domain and activates a RecA monomer for polymerization.

journal_name

J Mol Biol

authors

Lucarelli D,Wang YA,Galkin VE,Yu X,Wigley DB,Egelman EH

doi

10.1016/j.jmb.2009.06.042

subject

Has Abstract

pub_date

2009-08-14 00:00:00

pages

269-74

issue

2

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(09)00762-1

journal_volume

391

pub_type

杂志文章
  • Structural analysis of the group II intron splicing factor CRS2 yields insights into its protein and RNA interaction surfaces.

    abstract::Chloroplast RNA splicing 2 (CRS2) is a nuclear-encoded protein required for the splicing of nine group II introns in maize chloroplasts. CRS2 functions in the context of splicing complexes that include one of two CRS2-associated factors (CAF1 and CAF2). The CRS2-CAF1 and CRS2-CAF2 complexes are required for the splici...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.10.032

    authors: Ostheimer GJ,Hadjivassiliou H,Kloer DP,Barkan A,Matthews BW

    更新日期:2005-01-07 00:00:00

  • β-Structure within the Denatured State of the Helical Protein Domain BBL.

    abstract::Protein denatured states are the origin of both healthy and toxic conformational species. Denatured states of ultrafast folding proteins are of interest in mechanistic studies because they are energetically close to the kinetic bottleneck of folding. However, their transient nature makes them elusive to experiment. He...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2015.08.007

    authors: Thukral L,Schwarze S,Daidone I,Neuweiler H

    更新日期:2015-09-25 00:00:00

  • Plasminogen activator inhibitor-2 is highly tolerant to P8 residue substitution--implications for serpin mechanistic model and prediction of nsSNP activities.

    abstract::The serine protease inhibitor (serpin) superfamily is involved in a wide range of cellular processes including fibrinolysis, angiogenesis, apoptosis, inflammation, metastasis and viral pathogenesis. Here, we investigate the unique mousetrap inhibition mechanism of serpins through saturation mutagenesis of the P8 resid...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.09.008

    authors: Di Giusto DA,Sutherland AP,Jankova L,Harrop SJ,Curmi PM,King GC

    更新日期:2005-11-11 00:00:00

  • High affinity of endonuclease VII for the Holliday structure containing one nick ensures productive resolution.

    abstract::During homologous recombination, genetic information is physically exchanged between parental DNAs via crossing single strands of the same polarity within a four-way DNA junction called a Holliday structure. This process is terminated by the endonucleolytic activity of resolvases, which convert the four-way DNA back t...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/s0022-2836(02)00594-6

    authors: Birkenbihl RP,Kemper B

    更新日期:2002-08-02 00:00:00

  • Crystal structure of cardiac troponin C regulatory domain in complex with cadmium and deoxycholic acid reveals novel conformation.

    abstract::The amino-terminal regulatory domain of cardiac troponin C (cNTnC) plays an important role as the calcium sensor for the troponin complex. Calcium binding to cNTnC results in conformational changes that trigger a cascade of events that lead to cardiac muscle contraction. The cardiac N-terminal domain of TnC consists o...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.08.049

    authors: Li AY,Lee J,Borek D,Otwinowski Z,Tibbits GF,Paetzel M

    更新日期:2011-10-28 00:00:00

  • The N-terminal domains of myosin binding protein C can bind polymorphically to F-actin.

    abstract::The regulation of vertebrate striated muscle contraction involves a number of different molecules, including the thin-filament accessory proteins tropomyosin and troponin that provide Ca(2+)-dependent regulation by controlling access to myosin binding sites on actin. Cardiac myosin binding protein C (cMyBP-C) appears ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2011.07.056

    authors: Orlova A,Galkin VE,Jeffries CM,Egelman EH,Trewhella J

    更新日期:2011-09-23 00:00:00

  • Mitochondrial DNA variant in COX1 subunit significantly alters energy metabolism of geographically divergent wild isolates in Caenorhabditis elegans.

    abstract::Mitochondrial DNA (mtDNA) sequence variation can influence the penetrance of complex diseases and climatic adaptation. While studies in geographically defined human populations suggest that mtDNA mutations become fixed when they have conferred metabolic capabilities optimally suited for a specific environment, it has ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2014.02.009

    authors: Dingley SD,Polyak E,Ostrovsky J,Srinivasan S,Lee I,Rosenfeld AB,Tsukikawa M,Xiao R,Selak MA,Coon JJ,Hebert AS,Grimsrud PA,Kwon YJ,Pagliarini DJ,Gai X,Schurr TG,Hüttemann M,Nakamaru-Ogiso E,Falk MJ

    更新日期:2014-05-29 00:00:00

  • Sequences within Pr160gag-pol affecting the selective packaging of primer tRNA(Lys3) into HIV-1.

    abstract::The selective packaging of the primer tRNA(Lys3) into HIV-1 particles is dependent upon the viral incorporation of the Pr160gag-pol precursor protein. In order to map a tRNA(Lys3) binding site within this precursor, we have studied the effects of mutations in Pr160gag-pol upon the selective incorporation of tRNA(Lys3)...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3709

    authors: Khorchid A,Javanbakht H,Wise S,Halwani R,Parniak MA,Wainberg MA,Kleiman L

    更新日期:2000-05-26 00:00:00

  • Knowledge-based scoring function to predict protein-ligand interactions.

    abstract::The development and validation of a new knowledge-based scoring function (DrugScore) to describe the binding geometry of ligands in proteins is presented. It discriminates efficiently between well-docked ligand binding modes (root-mean-square deviation <2.0 A with respect to a crystallographically determined reference...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3371

    authors: Gohlke H,Hendlich M,Klebe G

    更新日期:2000-01-14 00:00:00

  • Characterization of preferred deoxyribonuclease I cleavage sites.

    abstract::The preferred DNase I cleavage sites within the 160 bp tyrT DNA fragment were identified by studying the initial rate of cleavage of individual bonds. The results show that there is no correlation between the rate of cleavage and the identity of the dinucleotide sequence that is cleaved. Examination of the sequences s...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1994.1152

    authors: Herrera JE,Chaires JB

    更新日期:1994-02-18 00:00:00

  • Alanine scanning of MS2 coat protein reveals protein-phosphate contacts involved in thermodynamic hot spots.

    abstract::The co-crystal structure of the MS2 coat protein dimer with its RNA operator reveals eight amino acid side-chains contacting seven of the RNA phosphates. These eight amino acids and five nearby control positions were individually changed to an alanine residue and the binding affinities of the mutant proteins to the RN...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.11.046

    authors: Hobson D,Uhlenbeck OC

    更新日期:2006-02-24 00:00:00

  • Monitoring sequence space as a test for the target of selection in viruses.

    abstract::An essential feature of viral quasispecies, predicted from quasispecies theory, is that the target of selection is the mutant distribution as a whole. To test molecularly the mutant composition selected from a viral quasispecies we reconstructed a mutant distribution using 19 antigenic variants of foot-and-mouth disea...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.10.066

    authors: Perales C,Martín V,Ruiz-Jarabo CM,Domingo E

    更新日期:2005-01-21 00:00:00

  • Primate evolution of the alpha-globin gene cluster and its Alu-like repeats.

    abstract::The arrangement of alpha-globin genes in Old World and New World monkeys and a prosimian, galago, has been determined by restriction mapping. Recombinant DNAs containing galago and Old World monkey alpha-globin genes have been isolated and subjected to a partial sequence determination for comparison to alpha-globin ge...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(86)90022-7

    authors: Sawada I,Schmid CW

    更新日期:1986-12-20 00:00:00

  • MPTherm-Pred: Analysis and Prediction of Thermal Stability Changes upon Mutations in Transmembrane Proteins.

    abstract::The stability of membrane proteins differs from globular proteins due to the presence of nonpolar membrane-spanning regions. Using a dataset of 929 membrane protein mutations whose effects on thermal stability (ΔTm) were experimentally determined, we found that the average ΔTm due to 190 stabilizing and 232 destabiliz...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章,评审

    doi:10.1016/j.jmb.2020.09.005

    authors: Kulandaisamy A,Zaucha J,Frishman D,Gromiha MM

    更新日期:2020-09-10 00:00:00

  • Crystal structure of LAAO from Calloselasma rhodostoma with an L-phenylalanine substrate: insights into structure and mechanism.

    abstract::L-Amino acid oxidase is a dimeric glycosylated flavoenzyme, a major constituent of the venom-from the snake Calloselasma rhodostoma. The enzyme exhibits apoptosis inducing effects as well as antibacterial and anti-HIV activities. The structure of l-amino acid oxidase with its substrate (L-phenylalanine) has been refin...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.09.032

    authors: Moustafa IM,Foster S,Lyubimov AY,Vrielink A

    更新日期:2006-12-15 00:00:00

  • Regulation of prion protein expression by noncoding regions of the Prnp gene.

    abstract::Expression of the cellular prion protein is necessary for the transmission and propagation of prion diseases. Increasing the level of prion protein expression decreases the incubation period for these diseases. Therefore, understanding the regulation of prion protein expression could be critical for treating or preven...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2007.02.086

    authors: Haigh CL,Wright JA,Brown DR

    更新日期:2007-05-11 00:00:00

  • The crystal structure of the actin binding domain from alpha-actinin in its closed conformation: structural insight into phospholipid regulation of alpha-actinin.

    abstract::Alpha-actinin is the major F-actin crosslinking protein in both muscle and non-muscle cells. We report the crystal structure of the actin binding domain of human muscle alpha-actinin-3, which is formed by two consecutive calponin homology domains arranged in a "closed" conformation. Structural studies and available bi...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2005.01.002

    authors: Franzot G,Sjöblom B,Gautel M,Djinović Carugo K

    更新日期:2005-04-22 00:00:00

  • The C-terminal region of cytoplasmic polyadenylation element binding protein is a ZZ domain with potential for protein-protein interactions.

    abstract::Cytoplasmic polyadenylation element binding protein (CPEB) provides temporal and spatial control of protein synthesis required for early development and neuronal synaptic plasticity. CPEB regulates protein expression by inhibiting polyadenylation of selected mRNA transcripts, which prevents binding of the ribosome for...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2013.03.009

    authors: Merkel DJ,Wells SB,Hilburn BC,Elazzouzi F,Pérez-Alvarado GC,Lee BM

    更新日期:2013-06-12 00:00:00

  • Intramolecular DNA triplexes, bent DNA and DNA unwinding elements in the initiation region of an amplified dihydrofolate reductase replicon.

    abstract::The nucleotide sequence of 6.2 kb (1 kb = 10(3) base-pairs) of DNA that encompasses the earliest replicating portion of the amplified dihydrofolate reductase domains of CHOC 400 cells has been determined. Origin region DNA contains two AluI family repeats, a novel repetitive element (termed ORR-1), a TGGGT-rich region...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(90)90008-A

    authors: Caddle MS,Lussier RH,Heintz NH

    更新日期:1990-01-05 00:00:00

  • Analysis of the tobacco chloroplast DNA replication origin (oriB) downstream of the 23 S rRNA gene.

    abstract::We have mapped the origin of DNA replication (oriB) downstream of the 23 S rRNA gene in each copy of the inverted repeat (IR) of tobacco chloroplast DNA between positions 130,502 and 131,924 (IR(A)) by a combination of approaches. In vivo chloroplast DNA replication intermediates were examined by two-dimensional agaro...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1997.0972

    authors: Kunnimalaiyaan M,Shi F,Nielsen BL

    更新日期:1997-05-02 00:00:00

  • Point mutations in the HIV-1 matrix protein turn off the myristyl switch.

    abstract::During the late phase of human immunodeficiency virus type-1 (HIV-1) replication, newly synthesized retroviral Gag proteins are targeted to lipid raft regions of specific cellular membranes, where they assemble and bud to form new virus particles. Gag binds preferentially to the plasma membrane (PM) of most hematopoie...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2006.11.068

    authors: Saad JS,Loeliger E,Luncsford P,Liriano M,Tai J,Kim A,Miller J,Joshi A,Freed EO,Summers MF

    更新日期:2007-02-16 00:00:00

  • Active transcription is required for maintenance of epigenetic memory in the malaria parasite Plasmodium falciparum.

    abstract::The most severe form of human malaria is caused by the protozoan parasite Plasmodium falciparum. The primary antigenic and virulence determinant expressed on the surface of infected red blood cells is PfEMP1 (P. falciparum erythrocyte membrane protein 1), a protein that mediates adhesion and sequestration of the paras...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2008.07.015

    authors: Dzikowski R,Deitsch KW

    更新日期:2008-10-03 00:00:00

  • Dimer form of phosphorylated Spo0A, a transcriptional regulator, stimulates the spo0F transcription at the initiation of sporulation in Bacillus subtilis.

    abstract::The Spo0A protein of Bacillus subtilis is a transcriptional regulator that shows extensive homology to the regulator proteins in bacterial two-component regulatory systems. Phosphorylation of Spo0A is absolutely necessary for the initiation of sporulation. We now show that phospho-Spo0A is a dimer, binds specifically ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1995.0354

    authors: Asayama M,Yamamoto A,Kobayashi Y

    更新日期:1995-06-30 00:00:00

  • A conserved element in the yeast RNase MRP RNA subunit can participate in a long-range base-pairing interaction.

    abstract::RNase MRP is a ribonucleoprotein endoribonuclease involved in eukaryotic pre-rRNA processing. The enzyme possesses a putatively catalytic RNA subunit, structurally related to that of RNase P. A thorough structure analysis of Saccharomyces cerevisiae MRP RNA, entailing enzymatic and chemical probing, mutagenesis and th...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/j.jmb.2004.05.076

    authors: Walker SC,Avis JM

    更新日期:2004-08-06 00:00:00

  • Sigma competition: the contest between bacteriophage T4 middle and late transcription.

    abstract::In bacterial transcription, diverse sigma-family promoter recognition proteins compete for a common RNA polymerase core. Bacteriophage T4 infection ultimately reduces this competition to a duel between activated viral middle and enhanced late transcription, involving two sigma proteins, two phage-encoded activator pro...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.2953

    authors: Kolesky S,Ouhammouch M,Brody EN,Geiduschek EP

    更新日期:1999-08-13 00:00:00

  • Recruiting Zn2+ to mediate potent, specific inhibition of serine proteases.

    abstract::As regulators of ubiquitous biological processes, serine proteases can cause disease states when inappropriately expressed or regulated, and are thus rational targets for inhibition by drugs. Recently we described a new inhibition mechanism applicable for the development of potent, selective small molecule serine prot...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.1999.3071

    authors: Katz BA,Luong C

    更新日期:1999-09-24 00:00:00

  • Topology of the components of the DNA packaging machinery in the phage phi29 prohead.

    abstract::Chromosome condensation inside dsDNA viral particles is a complex process requiring the coordinated action of several viral components. The similarity of the process in different viral systems has led to the suggestion that there is a common underlying mechanism for DNA packaging, in which the portal vertex or connect...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.3712

    authors: Ibarra B,Castón JR,Llorca O,Valle M,Valpuesta JM,Carrascosa JL

    更新日期:2000-05-19 00:00:00

  • FLP recombinase of the 2 microns circle plasmid of Saccharomyces cerevisiae bends its DNA target. Isolation of FLP mutants defective in DNA bending.

    abstract::The FLP recombinase is encoded by the yeast plasmid 2 microns circle and catalyses a site-specific recombination reaction that results in inversion of a segment of the 2 micron plasmid. We describe a method for the isolation of inactivating mutations in the FLP gene. The analysis of the recombination and binding activ...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/0022-2836(89)90310-0

    authors: Schwartz CJ,Sadowski PD

    更新日期:1989-02-20 00:00:00

  • Multiple roles of prolyl residues in structure and folding.

    abstract::To explore the ways that proline residues may influence the conformational options of a polypeptide backbone, we have characterized Pro-->Ala mutants of cellular retinoic acid-binding protein I (CRABP I). While all three Xaa-Pro bonds are in the trans conformation in the native protein and the equilibrium stability of...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1006/jmbi.2000.4002

    authors: Eyles SJ,Gierasch LM

    更新日期:2000-08-18 00:00:00

  • Resolution of a disordered region at the entrance of the human sex hormone-binding globulin steroid-binding site.

    abstract::The crystal structure of human sex hormone-binding globulin (SHBG) has revealed how 5alpha-dihydrotestosterone intercalates between the two seven-stranded beta-sheets of its amino-terminal laminin G-like domain. However, a region of disorder (residues 130 to 135 of SHBG) was identified together with a zinc-binding sit...

    journal_title:Journal of molecular biology

    pub_type: 杂志文章

    doi:10.1016/S0022-2836(02)00169-9

    authors: Grishkovskaya I,Avvakumov GV,Hammond GL,Muller YA

    更新日期:2002-05-03 00:00:00