当前位置： SCI文献检索 > JOURNAL OF MOLECULAR BIOLOGY期刊下所有文献 > The homologous pairing domain of RecA also mediates the allosteric regulation of DNA binding and ATP hydrolysis: a remarkable concentration of functional residues.

The homologous pairing domain of RecA also mediates the allosteric regulation of DNA binding and ATP hydrolysis: a remarkable concentration of functional residues.

Abstract：

:Switching between the active (ATP and DNA bound) and inactive conformations of the homologous recombination RecA protein is regulated by ATP hydrolysis. First, we use the homologous pairing domain of RecA derived from its mobile loop L2 to show that the interaction of this random coil peptide with the gamma-phosphate of ATP results in a peptide beta-conformation similar to that previously shown to be induced by DNA binding. Next, we show that in the whole RecA protein two residues in this L2 domain, Gln194 and Arg196, are catalytic amino acid residues for ATP hydrolysis and functionally resemble the corresponding residues engaged in GTP hydrolysis by two distinct classes of G proteins. Finally, we show that the role of DNA and high salt in the stimulation of the ATPase of RecA is to stabilize this highly mobile region involved in hydrolysis. This is a role similar to that described for RGSs in the activation of the GTPase of heterotrimeric G proteins. Therefore, (i) a prototypical DNA-dependent ATPase and ATP-stimulated DNA-binding protein, RecA, and eukaryotic signaling proteins share common stereochemical regulatory mechanisms; and (ii) in a remarkable example of parsimony, loop L2 is a molecular switch that controls both ATP promoted DNA binding and pairing reactions and DNA stimulated ATP hydrolysis.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Voloshin ON,Wang L,Camerini-Otero RD

doi

10.1006/jmbi.2000.4163

keywords:

subject

Has Abstract

pub_date

2000-11-10 00:00:00

pages

709-20

issue

5

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(00)94163-9

journal_volume

303

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR BIOLOGY文献大全
  • Structural studies on the Pseudomonas aeruginosa sialidase-like enzyme PA2794 suggest substrate and mechanistic variations.

    abstract：:Pseudomonas aeruginosa encodes an enzyme (PA2794) that is annotated as a sialidase (or neuraminidase), as it possesses three bacterial neuraminidase repeats that are a signature of nonviral sialidases. A recent report showed that when the gene encoding this sialidase is knocked out, this led to a reduction in biofilm ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2008.12.084

    authors： Xu G,Ryan C,Kiefel MJ,Wilson JC,Taylor GL

    更新日期：2009-02-27 00:00:00

  • Recruitment, Duplex Unwinding and Protein-Mediated Inhibition of the Dead-Box RNA Helicase Dbp2 at Actively Transcribed Chromatin.

    abstract：:RNA helicases play fundamental roles in modulating RNA structures and facilitating RNA-protein (RNP) complex assembly in vivo. Previously, our laboratory demonstrated that the DEAD-box RNA helicase Dbp2 in Saccharomyces cerevisiae is required to promote efficient assembly of the co-transcriptionally associated mRNA-bi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2016.02.005

    authors： Ma WK,Paudel BP,Xing Z,Sabath IG,Rueda D,Tran EJ

    更新日期：2016-03-27 00:00:00

  • The crystal structure of annexin A8 is similar to that of annexin A3.

    abstract：:Annexin A8 is a relatively infrequent and poorly studied member of this large family of calcium-binding and membrane-binding proteins. It is, however, associated with a specific disease, acute promyelocytic leukemia. We have solved its three-dimensional structure, which includes a moderately long and intact N terminus...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.11.015

    authors： Réty S,Sopková-de Oliveira Santos J,Dreyfuss L,Blondeau K,Hofbauerová K,Raguénès-Nicol C,Kerboeuf D,Renouard M,Russo-Marie F,Lewit-Bentley A

    更新日期：2005-02-04 00:00:00

  • Peptide models of local and long-range interactions in the molten globule state of human alpha-lactalbumin.

    abstract：:alpha-Lactalbumin, a small calcium-binding protein, forms an equilibrium molten globule state under a variety of conditions. A set of four peptides designed to probe the role of local interactions and the role of potential long-range interactions in stabilizing the molten globule of alpha-lactalbumin has been prepared...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2099

    authors： Demarest SJ,Fairman R,Raleigh DP

    更新日期：1998-01-01 00:00:00

  • Effect of the Asn52----Ile mutation on the redox potential of yeast cytochrome c. Theory and experiment.

    abstract：:Theoretical methods for correlation of sequence changes and redox potential of electron transport proteins are examined using the Asn52----Ile mutation in cytochrome c as a test case. The first approach uses the protein dipoles Langevin dipoles (PDLD) method and the high resolution X-ray structures of the native and t...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(92)90546-v

    authors： Langen R,Brayer GD,Berghuis AM,McLendon G,Sherman F,Warshel A

    更新日期：1992-04-05 00:00:00

  • Three-dimensional structure of a cloning vector. X-ray diffraction studies of filamentous bacteriophage M13 at 7 A resolution.

    abstract：:Filamentous bacteriophage M13 is a single-stranded DNA phage about 65 A in diameter and 9300 A long. X-ray diffraction studies of magnetically oriented fibers of native, mercury and iodine-labeled phage particles have been used to determine the arrangement of the major coat protein, the gene 8 product, in the virion. ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(92)90960-r

    authors： Glucksman MJ,Bhattacharjee S,Makowski L

    更新日期：1992-07-20 00:00:00

  • The binding of 2-deoxy-D-glucose 6-phosphate to glycogen phosphorylase b: kinetic and crystallographic studies.

    abstract：:Kinetic and crystallographic studies have characterized the effect of 2-deoxy-glucose 6-phosphate on the catalytic and structural properties of glycogen phosphorylase b. Previous work on the binding of glucose 6-phosphate, a potent physiological inhibitor of the enzyme, to T state phosphorylase b in the crystal showed...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1995.0665

    authors： Oikonomakos NG,Zographos SE,Johnson LN,Papageorgiou AC,Acharya KR

    更新日期：1995-12-15 00:00:00

  • Crystallization and preliminary crystallographic investigations of the soluble glucose dehydrogenase from Acinetobacter calcoaceticus.

    abstract：:Single crystals of the soluble glucose dehydrogenase (GDH) from Acinetobacter calcoaceticus have been grown by the vapour diffusion method. These crystals diffract to beyond 2.1 A and are suitable for X-ray crystallography. The space group was determined to be P2(1) with unit cell parameters a = 55.5 A, b = 104.5 A, c...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1553

    authors： Schlunegger MP,Grütter MG,Streiff MB,Olsthoorn AJ,Duine JA

    更新日期：1993-10-20 00:00:00

  • Molecular symmetry of the ClpP component of the ATP-dependent Clp protease, an Escherichia coli homolog of 20 S proteasome.

    abstract：:The ClpP component Clp protease from Escherichia coli has been crystallized and examined by X-ray crystallography and self-rotation function calculations. The crystal belongs to the monoclinic space group P2(1) with unit cell dimensions of a = 196.9 A, b = 104.3 A, c = 162.4 A and beta = 98.3 degrees. The X-ray diffra...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0499

    authors： Shin DH,Lee CS,Chung CH,Suh SW

    更新日期：1996-09-20 00:00:00

  • Crystal structure of human class mu glutathione transferase GSTM2-2. Effects of lattice packing on conformational heterogeneity.

    abstract：:The structures of three crystal forms of the class mu human glutathione transferase GSTM2-2 have been determined. X-ray phase information was obtained independently from molecular replacement and from anomalous scattering by a single isomorphous derivative. One crystal form contains a single monomer in the asymmetric ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1336

    authors： Raghunathan S,Chandross RJ,Kretsinger RH,Allison TJ,Penington CJ,Rule GS

    更新日期：1994-05-20 00:00:00

  • The chromosome of Shigella flexneri bacteriophage Sf6: complete nucleotide sequence, genetic mosaicism, and DNA packaging.

    abstract：:Shigella flexneri temperate bacteriophage Sf6 is of interest in part because its prophage expresses the oac gene that alters the antigenic properties of the surface O-antigen polysaccharide of its host bacterium. We have determined the complete sequence of its 39,044 bp genome. The sequence shows that Sf6 is a member ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2004.03.068

    authors： Casjens S,Winn-Stapley DA,Gilcrease EB,Morona R,Kühlewein C,Chua JE,Manning PA,Inwood W,Clark AJ

    更新日期：2004-05-28 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

    doi：10.1006/jmbi.1994.1258

    authors： Yang AS,Honig B

    更新日期：1994-04-15 00:00:00

  • Cubic phases of lipid-containing systems. A translational diffusion study by fluorescence recovery after photobleaching.

    abstract：:The lateral diffusion coefficient of fluorescent lipid analogues incorporated in four cubic phases of lipid-water systems was determined by the modulated fringe pattern photobleaching technique. In two of the phases, Q230 and Q224, whose structure is bicontinuous, the diffusion is almost as fast as in the fluid lipid ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1993.1051

    authors： Cribier S,Gulik A,Fellmann P,Vargas R,Devaux PF,Luzzati V

    更新日期：1993-01-20 00:00:00

  • The elastic I-band region of titin is assembled in a "modular" fashion by weakly interacting Ig-like domains.

    abstract：:The vertebrate striated muscle protein titin is thought to play a critical rôle in myofibril assembly and passive tension. The recently determined complete primary structure of titin revealed a modular architecture that opens the way to a structural characterisation and the understanding of essential properties of thi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1996.0050

    authors： Politou AS,Gautel M,Improta S,Vangelista L,Pastore A

    更新日期：1996-02-02 00:00:00

  • A dimer is the minimal proton-conducting unit of the influenza a virus M2 channel.

    abstract：:When influenza A virus infects host cells, its integral matrix protein M2 forms a proton-selective channel in the viral envelope. Although X-ray crystallography and NMR studies using fragment peptides have suggested that M2 stably forms a tetrameric channel irrespective of pH, the oligomeric states of the full-length ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2014.05.002

    authors： Kawano K,Yano Y,Matsuzaki K

    更新日期：2014-07-15 00:00:00

  • Three-dimensional structure of bovine NADH:ubiquinone oxidoreductase (complex I) at 22 A in ice.

    abstract：:NADH:ubiquinone oxidoreductase (complex I) is the first and largest complex in the electron transport chain of mitochondria. The bovine complex purified from cardiac muscle consists of at least 42 different subunits with a combined molecular mass of about 890 kDa. The three-dimensional structure of the complex was det...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.1668

    authors： Grigorieff N

    更新日期：1998-04-17 00:00:00

  • Accommodation of amino acid insertions in an alpha-helix of T4 lysozyme. Structural and thermodynamic analysis.

    abstract：:One to four alanines were inserted by site-directed mutagenesis at three different locations within the alpha-helix comprising residues 39 to 50 in bacteriophage T4 lysozyme. All insertion mutants were correctly folded and catalytically active although the insertions led to a thermal destabilization by 1.1 to 4.2 kcal...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1195

    authors： Heinz DW,Baase WA,Zhang XJ,Blaber M,Dahlquist FW,Matthews BW

    更新日期：1994-02-25 00:00:00

  • Transcriptional control in the EcoRI-F immunity region of Bacillus subtilis phage phi 105. Identification and unusual structure of the operator.

    abstract：:We present the first evidence, in Bacillus subtilis, for gene regulation through the classical mechanism of repressor-operator interaction. The EcoRI-F immunity region (immF) of lysogenic phage phi 105 contains two promoters, PM and PR, in divergent orientations. PM initiates transcription of the phi 105 repressor (c ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(87)90609-7

    authors： Van Kaer L,Van Montagu M,Dhaese P

    更新日期：1987-09-05 00:00:00

  • Crystallographic studies on damaged DNAs. II. N(6)-methoxyadenine can present two alternate faces for Watson-Crick base-pairing, leading to pyrimidine transition mutagenesis.

    abstract：:In a previous paper, 2'-deoxy-N(6)-methoxyadenosine (mo(6)A) was shown to form a mismatch base-pair with 2'-deoxycytidine with a Watson-Crick-type geometry. To fully understand the structural basis of genetic mutations with damaged DNA, it is necessary to examine whether the methoxylated adenine residue still has the ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1999.3304

    authors： Chatake T,Hikima T,Ono A,Ueno Y,Matsuda A,Takénaka A

    更新日期：1999-12-17 00:00:00

  • Primary structure of the second largest subunit of human RNA polymerase II (or B).

    abstract：:The cDNA of the second largest subunit of RNA polymerase II (or B) from HeLa cells has been cloned and sequenced. A predicted amino acid sequence of 1174 residues (calculated molecular mass of 133,896 Da) was derived from the longest open reading frame and compared to the sequences of homologous subunits of polymerase...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(92)91071-v

    authors： Acker J,Wintzerith M,Vigneron M,Kédinger C

    更新日期：1992-08-20 00:00:00

  • Crystallization and preliminary X-ray diffraction analysis of a type I beta-glucosidase encoded by the bgIA gene of Bacillus polymyxa.

    abstract：:The enzyme encoded by the bgIA gene of Bacillus polymyxa, a type I beta-glucosidase belonging to family I of glycosyl hydrolases, has been purified to homogeneity from an Escherichia coli culture which overexpressed the gene, and crystallized. The crystals, which diffract to 3.0 A resolution, belong to the orthorhombi...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1994.1441

    authors： Sanz-Aparicio J,Romero A,Martinez-Ripoll M,Madarro A,Flors A,Polaina J

    更新日期：1994-07-15 00:00:00

  • Molecular and structural basis for redox regulation of beta-actin.

    abstract：:An essential consequence of growth factor-mediated signal transduction is the generation of intracellular H(2)O(2). It operates as a second messenger in the control of actin microfilament dynamics, causing rapid and dramatic changes in the morphology and motile activity of stimulated cells. Little is understood about ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2007.04.056

    authors： Lassing I,Schmitzberger F,Björnstedt M,Holmgren A,Nordlund P,Schutt CE,Lindberg U

    更新日期：2007-07-06 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

  • Target Residence Time-Guided Optimization on TTK Kinase Results in Inhibitors with Potent Anti-Proliferative Activity.

    abstract：:The protein kinase threonine tyrosine kinase (TTK; also known as Mps1) is a critical component of the spindle assembly checkpoint and a promising drug target for the treatment of aggressive cancers, such as triple negative breast cancer. While the first TTK inhibitors have entered clinical trials, little is known abou...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2017.05.014

    authors： Uitdehaag JCM,de Man J,Willemsen-Seegers N,Prinsen MBW,Libouban MAA,Sterrenburg JG,de Wit JJP,de Vetter JRF,de Roos JADM,Buijsman RC,Zaman GJR

    更新日期：2017-07-07 00:00:00

  • Structures of Tyr188Leu mutant and wild-type HIV-1 reverse transcriptase complexed with the non-nucleoside inhibitor HBY 097: inhibitor flexibility is a useful design feature for reducing drug resistance.

    abstract：:The second generation Hoechst-Bayer non-nucleoside inhibitor, HBY 097 (S-4-isopropoxycarbonyl-6-methoxy-3-(methylthiomethyl)-3, 4-dihydroqui noxalin-2(1H)-thione), is an extremely potent inhibitor of HIV-1 reverse transcriptase (RT) and of HIV-1 infection in cell culture. HBY 097 selects for unusual drug-resistance mu...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2171

    authors： Hsiou Y,Das K,Ding J,Clark AD Jr,Kleim JP,Rösner M,Winkler I,Riess G,Hughes SH,Arnold E

    更新日期：1998-11-27 00:00:00

  • Specific RNA-binding antibodies with a four-amino-acid code.

    abstract：:Numerous large non-coding RNAs are rapidly being discovered, and many of them have been shown to play vital roles in gene expression, gene regulation, and human diseases. Given their often structured nature, specific recognition with an antibody fragment becomes feasible and may help define the structure and function ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2014.03.003

    authors： Sherman EM,Holmes S,Ye JD

    更新日期：2014-05-15 00:00:00

  • Characterization of in vitro and in vivo mutations in non-conserved nucleotides in the ribosomal RNA recognition domain for the ribotoxins ricin and sarcin and the translation elongation factors.

    abstract：:The sarcin/ricin domain in 23 S/28 S rRNA is crucial for ribosome function, since it constitutes at least part of the binding site for the elongation factors and hence is essential for binding aminoacyl-tRNA and for translocation. The domain is also the site of action of ricin and sarcin and analysis of the effect of ...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1006/jmbi.1998.2337

    authors： Macbeth MR,Wool IG

    更新日期：1999-01-15 00:00:00

  • Conformation of the coat protein of filamentous bacteriophage Pf1 determined by neutron diffraction from magnetically oriented gels of specifically deuterated virions.

    abstract：:The structure of filamentous bacteriophage Pf1 has been studied using neutron diffraction from magnetically oriented gels of native and valine-deuterated phage. Neutron diffraction intensities were measured to approximately 8 A resolution along the equator and first six layer-lines, and differences due to the deuterat...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/0022-2836(88)90387-7

    authors： Stark W,Glucksman MJ,Makowski L

    更新日期：1988-01-05 00:00:00

  • Combining EPR with fluorescence spectroscopy to monitor conformational changes at the myosin nucleotide pocket.

    abstract：:We used spin-labeled nucleotide analogs and fluorescence spectroscopy to monitor conformational changes at the nucleotide-binding site of wild-type Dictyostelium discoideum (WT) myosin and a construct containing a single tryptophan at position F239 near the switch 1 loop. Electron paramagnetic resonance (EPR) spectros...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2009.12.035

    authors： Naber N,Málnási-Csizmadia A,Purcell TJ,Cooke R,Pate E

    更新日期：2010-03-05 00:00:00

  • Long-range communications between DNA sites by the dimeric restriction endonuclease SgrAI.

    abstract：:The SgrAI endonuclease displays its maximal activity on DNA with two copies of its recognition sequence, cleaving both sites concertedly. While most restriction enzymes that act concurrently at two sites are tetramers, SgrAI is a dimer in solution. Its reaction at two cognate sites involves the association of two DNA-...

    journal_title：Journal of molecular biology

    pub_type： 杂志文章

    doi：10.1016/j.jmb.2005.04.053

    authors： Wood KM,Daniels LE,Halford SE

    更新日期：2005-07-08 00:00:00