当前位置： SCI文献检索 > NUCLEIC ACIDS RESEARCH期刊下所有文献 > Differential modes of DNA binding by mismatch uracil DNA glycosylase from Escherichia coli: implications for abasic lesion processing and enzyme communication in the base excision repair pathway.

Differential modes of DNA binding by mismatch uracil DNA glycosylase from Escherichia coli: implications for abasic lesion processing and enzyme communication in the base excision repair pathway.

Abstract：

:Mismatch uracil DNA glycosylase (Mug) from Escherichia coli is an initiating enzyme in the base-excision repair pathway. As with other DNA glycosylases, the abasic product is potentially more harmful than the initial lesion. Since Mug is known to bind its product tightly, inhibiting enzyme turnover, understanding how Mug binds DNA is of significance when considering how Mug interacts with downstream enzymes in the base-excision repair pathway. We have demonstrated differential binding modes of Mug between its substrate and abasic DNA product using both band shift and fluorescence anisotropy assays. Mug binds its product cooperatively, and a stoichiometric analysis of DNA binding, catalytic activity and salt-dependence indicates that dimer formation is of functional significance in both catalytic activity and product binding. This is the first report of cooperativity in the uracil DNA glycosylase superfamily of enzymes, and forms the basis of product inhibition in Mug. It therefore provides a new perspective on abasic site protection and the findings are discussed in the context of downstream lesion processing and enzyme communication in the base excision repair pathway.

journal_name

Nucleic Acids Res

journal_title

Nucleic acids research

authors

Grippon S,Zhao Q,Robinson T,Marshall JJ,O'Neill RJ,Manning H,Kennedy G,Dunsby C,Neil M,Halford SE,French PM,Baldwin GS

doi

10.1093/nar/gkq913

subject

Has Abstract

pub_date

2011-04-01 00:00:00

pages

2593-603

issue

7

eissn

0305-1048

issn

1362-4962

pii

gkq913

journal_volume

39

pub_type

杂志文章

相关文献

NUCLEIC ACIDS RESEARCH文献大全
  • Transcription of cloned Moloney murine leukemia proviral DNA injected into Xenopus laevis oocytes.

    abstract：:We have microinjected genomic DNA clones containing the Moloney murine leukemia virus (M-MuLV) proviral genome and flanking mouse sequences from Mov-3, Mov-7 and Mov-10 mice into Xenopus laevis oocytes and analyzed the virus-specific transcription and translation products. These mouse strains carry a proviral genome c...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/11.12.3989

    authors： Breindl M,Kalthoff H,Jaenisch R

    更新日期：1983-06-25 00:00:00

  • Fission yeast with DNA polymerase delta temperature-sensitive alleles exhibits cell division cycle phenotype.

    abstract：:DNA polymerases alpha and delta are essential enzymes believed to play critical roles in initiation and replication of chromosome DNA. In this study, we show that the genes for Schizosaccharomyces pombe (S.pombe) DNA polymerase alpha and delta (pol alpha+ and pol delta+) are essential for cell viability. Disruption of...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/21.16.3821

    authors： Francesconi S,Park H,Wang TS

    更新日期：1993-08-11 00:00:00

  • Bacillus subtilis RecN binds and protects 3'-single-stranded DNA extensions in the presence of ATP.

    abstract：:Bacillus subtilis RecN appears to be an early detector of breaks in double-stranded DNA. In vivo, RecN forms discrete nucleoid-associated structures and in vitro exhibits Mg2+-dependent single-stranded (ss) DNA binding and ssDNA-dependent ATPase activities. In the presence of ATP or ADP, RecN assembles to form large n...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gki533

    authors： Sanchez H,Alonso JC

    更新日期：2005-04-22 00:00:00

  • Isolation of molecular markers from specific chromosomal intervals using DNA pools from existing mapping populations.

    abstract：:We present a general method for isolating molecular markers specific to any region of a chromosome using existing mapping populations. Two pools of DNA from individuals homozygous for opposing alleles for a targeted chromosomal interval, defined by two or more linked RFLP markers, are constructed from members of an ex...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/19.23.6553

    authors： Giovannoni JJ,Wing RA,Ganal MW,Tanksley SD

    更新日期：1991-12-11 00:00:00

  • Binding of an RNA aptamer and a partial peptide of a prion protein: crucial importance of water entropy in molecular recognition.

    abstract：:It is a central issue to elucidate the new type of molecular recognition accompanied by a global structural change of a molecule upon binding to its targets. Here we investigate the driving force for the binding of R12 (a ribonucleic acid aptamer) and P16 (a partial peptide of a prion protein) during which P16 exhibit...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gku382

    authors： Hayashi T,Oshima H,Mashima T,Nagata T,Katahira M,Kinoshita M

    更新日期：2014-06-01 00:00:00

  • Direct sequencing of RAPD fragments using 3'-extended oligonucleotide primers and dye terminator cycle-sequencing.

    abstract：:Random amplified polymorphic DNA (RAPD) markers are used widely to develop high resolution genetic maps and for genome fingerprinting. Typically, single oligomers of approximately 10 nucleotides are used to PCR amplify characteristic RAPD marker fragments. We describe an efficient method for the direct end-sequencing ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/27.19.e28

    authors： Mitchelson KR,Drenth J,Duong H,Chaparro JX

    更新日期：1999-10-01 00:00:00

  • Gene organization of the small subunit of human calcium-activated neutral protease.

    abstract：:The gene for the small subunit of human calcium-activated neutral protease was isolated and sequenced. It is 11 kb long and comprises 11 exons. No TATA or CAT box was found upstream of the possible transcription initiation sites, but there are three so-called G-C box sequences and one G-C box-like sequence, which are ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/14.22.8805

    authors： Miyake S,Emori Y,Suzuki K

    更新日期：1986-11-25 00:00:00

  • GWIDD: Genome-wide protein docking database.

    abstract：:Structural information on interacting proteins is important for understanding life processes at the molecular level. Genome-wide docking database is an integrated resource for structural studies of protein-protein interactions on the genome scale, which combines the available experimental data with models obtained by ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkp944

    authors： Kundrotas PJ,Zhu Z,Vakser IA

    更新日期：2010-01-01 00:00:00

  • On the specificity and effects on transcription of P-element insertions at the yellow locus of Drosophila melanogaster.

    abstract：:Fourteen P-element insertion mutants at the yellow (y) gene of D. melanogaster have been analysed by restriction mapping and DNA sequencing. The distribution of the insertion sites is nonrandom, with a preferred target site in the 5'-transcribed but non-translated leader of the gene. Transcription analysis indicates t...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/16.7.3039

    authors： Howes G,O'Connor M,Chia W

    更新日期：1988-04-11 00:00:00

  • Nucleotide sequence of the narL gene that is involved in global regulation of nitrate controlled respiratory genes of Escherichia coli.

    abstract：:The DNA sequence was determined for the narL gene of Escherichia coli. This gene is involved in global regulation of a number of nitrate controlled genes including frdABCD, tor, narGHJI, and adhE which are associated with bacterial respiration and fermentation. Comparison of the deduced amino acid sequence of narL to ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/17.5.1965

    authors： Gunsalus RP,Kalman LV,Stewart RR

    更新日期：1989-03-11 00:00:00

  • The effects of polymorphisms on human gene targeting.

    abstract：:DNA mismatches that occur between vector homology arms and chromosomal target sequences reduce gene targeting frequencies in several species; however, this has not been reported in human cells. Here we demonstrate that even a single mismatched base pair can significantly decrease human gene targeting frequencies. In a...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkt1303

    authors： Deyle DR,Li LB,Ren G,Russell DW

    更新日期：2014-03-01 00:00:00

  • Affinity proteomic dissection of the human nuclear cap-binding complex interactome.

    abstract：:A 5',7-methylguanosine cap is a quintessential feature of RNA polymerase II-transcribed RNAs, and a textbook aspect of co-transcriptional RNA processing. The cap is bound by the cap-binding complex (CBC), canonically consisting of nuclear cap-binding proteins 1 and 2 (NCBP1/2). Interest in the CBC has recently renewed...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkaa743

    authors： Dou Y,Kalmykova S,Pashkova M,Oghbaie M,Jiang H,Molloy KR,Chait BT,Rout MP,Fenyö D,Jensen TH,Altukhov I,LaCava J

    更新日期：2020-10-09 00:00:00

  • Mitome: dynamic and interactive database for comparative mitochondrial genomics in metazoan animals.

    abstract：:Mitome is a specialized mitochondrial genome database designed for easy comparative analysis of various features of metazoan mitochondrial genomes such as base frequency, A+T skew, codon usage and gene arrangement pattern. A particular function of the database is the automatic reconstruction of phylogenetic relationsh...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkm763

    authors： Lee YS,Oh J,Kim YU,Kim N,Yang S,Hwang UW

    更新日期：2008-01-01 00:00:00

  • Structural basis for RNA-genome recognition during bacteriophage Qβ replication.

    abstract：:Upon infection of Escherichia coli by bacteriophage Qβ, the virus-encoded β-subunit recruits host translation elongation factors EF-Tu and EF-Ts and ribosomal protein S1 to form the Qβ replicase holoenzyme complex, which is responsible for amplifying the Qβ (+)-RNA genome. Here, we use X-ray crystallography, NMR spect...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkv1212

    authors： Gytz H,Mohr D,Seweryn P,Yoshimura Y,Kutlubaeva Z,Dolman F,Chelchessa B,Chetverin AB,Mulder FA,Brodersen DE,Knudsen CR

    更新日期：2015-12-15 00:00:00

  • FBXL5-mediated degradation of single-stranded DNA-binding protein hSSB1 controls DNA damage response.

    abstract：:Human single-strand (ss) DNA binding proteins 1 (hSSB1) has been shown to participate in DNA damage response and maintenance of genome stability by regulating the initiation of ATM-dependent signaling. ATM phosphorylates hSSB1 and prevents hSSB1 from ubiquitin-proteasome-mediated degradation. However, the E3 ligase th...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gku876

    authors： Chen ZW,Liu B,Tang NW,Xu YH,Ye XY,Li ZM,Niu XM,Shen SP,Lu S,Xu L

    更新日期：2014-10-01 00:00:00

  • Systematic analysis of enzymatic DNA polymerization using oligo-DNA templates and triphosphate analogs involving 2',4'-bridged nucleosides.

    abstract：:In order to systematically analyze the effects of nucleoside modification of sugar moieties in DNA polymerase reactions, we synthesized 16 modified templates containing 2',4'-bridged nucleotides and three types of 2',4'-bridged nucleoside-5'-triphospates with different bridging structures. Among the five types of ther...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkn404

    authors： Kuwahara M,Obika S,Nagashima J,Ohta Y,Suto Y,Ozaki H,Sawai H,Imanishi T

    更新日期：2008-08-01 00:00:00

  • Helicobacter pylori oriC--the first bipartite origin of chromosome replication in Gram-negative bacteria.

    abstract：:Binding of the DnaA protein to oriC leads to DNA melting within the DNA unwinding element (DUE) and initiates replication of the bacterial chromosome. Helicobacter pylori oriC was previously identified as a region localized upstream of dnaA and containing a cluster of DnaA boxes bound by DnaA protein with a high affin...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gks742

    authors： Donczew R,Weigel C,Lurz R,Zakrzewska-Czerwinska J,Zawilak-Pawlik A

    更新日期：2012-10-01 00:00:00

  • Fluorescence of 2-aminopurine reveals rapid conformational changes in the RB69 DNA polymerase-primer/template complexes upon binding and incorporation of matched deoxynucleoside triphosphates.

    abstract：:We have used 2-aminopurine (2AP) as a fluorescent probe in the template strand of a 13/20mer primer/template (D) to detect deoxynucleoside triphosphates (N)-dependent conformational changes exhibited by RB69 DNA polymerase (ED) complexes. The rates and amplitudes of fluorescence quenching depend hyperbolically on the ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkm587

    authors： Zhang H,Cao W,Zakharova E,Konigsberg W,De La Cruz EM

    更新日期：2007-01-01 00:00:00

  • Gene integrated set profile analysis: a context-based approach for inferring biological endpoints.

    abstract：:The identification of genes with specific patterns of change (e.g. down-regulated and methylated) as phenotype drivers or samples with similar profiles for a given gene set as drivers of clinical outcome, requires the integration of several genomic data types for which an 'integrate by intersection' (IBI) approach is ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkv1503

    authors： Kowalski J,Dwivedi B,Newman S,Switchenko JM,Pauly R,Gutman DA,Arora J,Gandhi K,Ainslie K,Doho G,Qin Z,Moreno CS,Rossi MR,Vertino PM,Lonial S,Bernal-Mizrachi L,Boise LH

    更新日期：2016-04-20 00:00:00

  • Genetic manipulation of an exogenous non-immunoglobulin protein by gene conversion machinery in a chicken B cell line.

    abstract：:During culture, a chicken B cell line DT40 spontaneously mutates immunoglobulin (Ig) genes by gene conversion, which involves activation-induced cytidine deaminase (AID)-dependent homologous recombination of the variable (V) region gene with upstream pseudo-V genes. To explore whether this mutation mechanism can targe...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gnj013

    authors： Kanayama N,Todo K,Takahashi S,Magari M,Ohmori H

    更新日期：2006-01-18 00:00:00

  • The human Obg protein GTPBP10 is involved in mitoribosomal biogenesis.

    abstract：:The human mitochondrial translation apparatus, which synthesizes the core subunits of the oxidative phosphorylation system, is of central interest as mutations in several genes encoding for mitoribosomal proteins or translation factors cause severe human diseases. Little is known, how this complex machinery assembles ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gky701

    authors： Lavdovskaia E,Kolander E,Steube E,Mai MM,Urlaub H,Richter-Dennerlein R

    更新日期：2018-09-19 00:00:00

  • BLAST2SRS, a web server for flexible retrieval of related protein sequences in the SWISS-PROT and SPTrEMBL databases.

    abstract：:SRS (Sequence Retrieval System) is a widely used keyword search engine for querying biological databases. BLAST2 is the most widely used tool to query databases by sequence similarity search. These tools allow users to retrieve sequences by shared keyword or by shared similarity, with many public web servers available...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkg535

    authors： Bimpikis K,Budd A,Linding R,Gibson TJ

    更新日期：2003-07-01 00:00:00

  • The nucleotide sequence of 5.8S rRNA from the posterior silk gland of the silkworm Philosamia cynthia ricini.

    abstract：:The nucleotide sequence of 5.8S rRNA from the Chinese silkworm Philosamia cynthia ricini has been determined by gel sequencing and mobility shift methods. The complete primary structure is (sequence in text). This is one of the largest known 5.8S rRNAs. As compared to Bombyx 5.8S rRNA, it is two nucleotides longer; t...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/10.20.6383

    authors： Feng YX,Krupp G,Gross HJ

    更新日期：1982-10-25 00:00:00

  • PlantLoc: an accurate web server for predicting plant protein subcellular localization by substantiality motif.

    abstract：:Knowledge of subcellular localizations (SCLs) of plant proteins relates to their functions and aids in understanding the regulation of biological processes at the cellular level. We present PlantLoc, a highly accurate and fast webserver for predicting the multi-label SCLs of plant proteins. The PlantLoc server has two...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkt428

    authors： Tang S,Li T,Cong P,Xiong W,Wang Z,Sun J

    更新日期：2013-07-01 00:00:00

  • BRENDA in 2015: exciting developments in its 25th year of existence.

    abstract：:The BRENDA enzyme information system (http://www.brenda-enzymes.org/) has developed into an elaborate system of enzyme and enzyme-ligand information obtained from different sources, combined with flexible query systems and evaluation tools. The information is obtained by manual extraction from primary literature, text...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gku1068

    authors： Chang A,Schomburg I,Placzek S,Jeske L,Ulbrich M,Xiao M,Sensen CW,Schomburg D

    更新日期：2015-01-01 00:00:00

  • The Gypsy Database (GyDB) of mobile genetic elements.

    abstract：:In this article, we introduce the Gypsy Database (GyDB) of mobile genetic elements, an in-progress database devoted to the non-redundant analysis and evolutionary-based classification of mobile genetic elements. In this first version, we contemplate eukaryotic Ty3/Gypsy and Retroviridae long terminal repeats (LTR) ret...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkm697

    authors： Lloréns C,Futami R,Bezemer D,Moya A

    更新日期：2008-01-01 00:00:00

  • rDNA in Locusta migratoria is very variable: two introns and extensive restriction site polymorphisms in the spacer.

    abstract：:Cloned ribosomal DNA (rDNA) of Locusta migratoria was analyzed by restriction site mapping and SI nuclease experiments. The repeat unit is 18 kb long. The nontranscribed spacer region (NTS) is very large (11 kb) and homogeneous in length, but many of the restriction sites are heterogeneous among the repeat units. Two ...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/13.4.1251

    authors： Schäfer M,Kunz W

    更新日期：1985-02-25 00:00:00

  • A novel human cytochrome P450 gene (P450IIB): chromosomal localization and evidence for alternative splicing.

    abstract：:We have isolated from a single human liver cDNA library two clones which are highly homologous (78% over the coding region) to the major phenobarbital-inducible P450 from rat (P450IIB1). This is the first direct demonstration of the presence of the P450IIB gene subfamily in humans. This subfamily is much less extensiv...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/16.13.5783

    authors： Miles JS,Spurr NK,Gough AC,Jowett T,McLaren AW,Brook JD,Wolf CR

    更新日期：1988-07-11 00:00:00

  • Role of LrpC from Bacillus subtilis in DNA transactions during DNA repair and recombination.

    abstract：:Bacillus subtilis LrpC is a sequence-independent DNA-binding and DNA-bending protein, which binds both single-stranded (ss) and double-stranded (ds) DNA and facilitates the formation of higher order protein-DNA complexes in vitro. LrpC binds at different sites within the same DNA molecule promoting intramolecular liga...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkj418

    authors： López-Torrejón G,Martínez-Jiménez MI,Ayora S

    更新日期：2006-01-10 00:00:00

  • Molecular characteristics of reiterative DNA unwinding by the Caenorhabditis elegans RecQ helicase.

    abstract：:The RecQ family of helicases is highly conserved both structurally and functionally from bacteria to humans. Defects in human RecQ helicases are associated with genetic diseases that are characterized by cancer predisposition and/or premature aging. RecQ proteins exhibit 3'-5' helicase activity and play critical roles...

    journal_title：Nucleic acids research

    pub_type： 杂志文章

    doi：10.1093/nar/gkz708

    authors： Choi S,Lee SW,Kim H,Ahn B

    更新日期：2019-10-10 00:00:00