DNA bending by M.EcoKI methyltransferase is coupled to nucleotide flipping. (Q24810294)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:15942026%20AND%20SRC:MED&resulttype=core&format=json

12 January 2020

title

DNA bending by M.EcoKI methyltransferase is coupled to nucleotide flipping (English)

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12 January 2020

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12 January 2020

Tsueu-Ju Su

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12 January 2020

Mark R Tock

series ordinal

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12 January 2020

Stefan U Egelhaaf

series ordinal

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12 January 2020

David T F Dryden

series ordinal

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12 January 2020

language of work or name

English

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publication date

7 June 2005

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12 January 2020

published in

Nucleic Acids Research

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12 January 2020

volume

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12 January 2020

issue

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12 January 2020

page(s)

3235-3244

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Type I restriction systems: sophisticated molecular machines (a legacy of Bertani and Weigle)

12 January 2020

cites work

1 reference

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2-Aminopurine as a fluorescent probe for DNA base flipping by methyltransferases

7 April 2017

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Structure of Ocr from bacteriophage T7, a protein that mimics B-form DNA

7 April 2017

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The structural basis of DNA target discrimination by papillomavirus E2 proteins

7 April 2017

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Coupling of local folding to site-specific binding of proteins to DNA

7 April 2017

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Factors Contributing to Aromatic Stacking in Water: Evaluation in the Context of DNA.

7 April 2017

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Initiation of translocation by Type I restriction-modification enzymes is associated with a short DNA extrusion

28 September 2017

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Structural evidence of a passive base-flipping mechanism for beta-glucosyltransferase

28 September 2017

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Unusual 2-aminopurine fluorescence from a complex of DNA and the EcoKI methyltransferase

28 September 2017

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Solution measurement of DNA curvature in papillomavirus E2 binding sites

28 September 2017

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Structural transitions and elasticity from torque measurements on DNA.

28 September 2017

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A mechanistic perspective on the chemistry of DNA repair glycosylases

28 September 2017

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Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase.

28 September 2017

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Interaction of the ocr gene 0.3 protein of bacteriophage T7 with EcoKI restriction/modification enzyme

28 September 2017

1 reference

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The papillomavirus E2 proteins: structure, function, and biology

28 September 2017

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Dynamic activation of protein function: a view emerging from NMR spectroscopy.

28 September 2017

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AdoMet-dependent methylation, DNA methyltransferases and base flipping

28 September 2017

1 reference

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Effects of DNA sequence and structure on binding of RecA to single-stranded DNA.

28 September 2017

1 reference

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The mechanism of DNA cytosine-5 methylation. Kinetic and mutational dissection of Hhai methyltransferase

28 September 2017

1 reference

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SfiI endonuclease activity is strongly influenced by the non-specific sequence in the middle of its recognition site

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

p53 C-terminal interaction with DNA ends and gaps has opposing effect on specific DNA binding by the core

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

Molecular enzymology of the EcoRV DNA-(Adenine-N (6))-methyltransferase: kinetics of DNA binding and bending, kinetic mechanism and linear diffusion of the enzyme on DNA.

28 September 2017

1 reference

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Thermodynamic and kinetic analyses for understanding sequence-specific DNA recognition

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

Binding of EcoP15I DNA methyltransferase to DNA reveals a large structural distortion within the recognition sequence

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

Estimating the persistence length of a worm-like chain molecule from force-extension measurements

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

The DNA binding characteristics of the trimeric EcoKI methyltransferase and its partially assembled dimeric form determined by fluorescence polarisation and DNA footprinting

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

Crystal structure of restriction endonuclease BglI bound to its interrupted DNA recognition sequence

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

Ionic effects on the elasticity of single DNA molecules

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

High resolution footprinting of a type I methyltransferase reveals a large structural distortion within the DNA recognition site

28 September 2017

1 reference

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Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules

28 September 2017

1 reference

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DNA recognition by the EcoK methyltransferase. The influence of DNA methylation and the cofactor S-adenosyl-L-methionine

28 September 2017

1 reference

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A mutational analysis of the two motifs common to adenine methyltransferases.

28 September 2017

1 reference

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DNA-binding induces a major structural transition in a type I methyltransferase.

28 September 2017

1 reference

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Melting of a DNA helix terminus within the active site of a DNA polymerase

28 September 2017

1 reference

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Protein fluctuations and the thermodynamic uncertainty principle

28 September 2017

1 reference

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Synthesis and properties of defined DNA oligomers containing base mispairs involving 2-aminopurine

28 September 2017

1 reference

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Mutations the confer de Novo activity upon a maintenance methyltransferase

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

The A. tumefaciens transcriptional activator OccR causes a bend at a target promoter, which is partially relaxed by a plant tumor metabolite

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

Importance of DNA stiffness in protein-DNA binding specificity

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

DNA bending by EcoRI DNA methyltransferase accelerates base flipping but compromises specificity

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

Measurement of the absolute temporal coupling between DNA binding and base flipping

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

Localization of a protein-DNA interface by random mutagenesis

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

Targeted base stacking disruption by the EcoRI DNA methyltransferase

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

Sequence-dependent differences in DNA structure influence the affinity of P22 operator for P22 repressor

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

Characterization of the DNA methylase activity of the restriction enzyme from Escherichia coli K

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

Cooperative binding of lambda repressors to sites separated by integral turns of the DNA helix

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

The mechanism of target base attack in DNA cytosine carbon 5 methylation

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

Stopped-flow and mutational analysis of base flipping by the Escherichia coli Dam DNA-(adenine-N6)-methyltransferase

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

HhaI DNA methyltransferase uses the protruding Gln237 for active flipping of its target cytosine.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

Simultaneous DNA binding, bending, and base flipping: evidence for a novel M.EcoRI methyltransferase-DNA complex

28 November 2018

1 reference

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The role of the minor groove substituents in indirect readout of DNA sequence by 434 repressor

28 November 2018

1 reference

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Base flipping in DNA: pathways and energetics studied with molecular dynamic simulations.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

Free energy and structural pathways of base flipping in a DNA GCGC containing sequence.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

Target recognition by EcoKI: the recognition domain is robust and restriction-deficiency commonly results from the proteolytic control of enzyme activity

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

Spontaneous base flipping in DNA and its possible role in methyltransferase binding

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

Purification and characterization of the methyltransferase from the type 1 restriction and modification system of Escherichia coli K12.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1143692

Reactions of BglI and other type II restriction endonucleases with discontinuous recognition sites

28 November 2018

1 reference

12 December 2020

Exciton and excimer formation in DNA at room temperature

1 reference

12 December 2020

Structural modelling of a type I DNA methyltransferase

1 reference

12 December 2020

Flexibility of single-stranded DNA: use of gapped duplex helices to determine the persistence lengths of poly(dT) and poly(dA)

1 reference

12 December 2020

The in vitro assembly of the EcoKI type I DNA restriction/modification enzyme and its in vivo implications

1 reference

12 December 2020

Pre-bending of a promoter sequence enhances affinity for the TATA-binding factor

1 reference

12 December 2020

Allostery without conformational change. A plausible model

1 reference

12 December 2020

Differential binding of the Escherichia coli HU, homodimeric forms and heterodimeric form to linear, gapped and cruciform DNA

1 reference

12 December 2020

Melting and premelting transitions of an oligomer measured by DNA base fluorescence and absorption

1 reference

12 December 2020

DNA structure and flexibility in the sequence-specific binding of papillomavirus E2 proteins

1 reference

12 December 2020

Sequence dependent rigidity of single stranded DNA

1 reference

12 December 2020

DNA sequence-specific recognition by the Saccharomyces cerevisiae "TATA" binding protein: promoter-dependent differences in the thermodynamics and kinetics of binding

1 reference

12 December 2020

Structural and thermodynamic strategies for site-specific DNA binding proteins

1 reference

12 December 2020

Specificity in Protein–DNA Interactions: Energetic Recognition by the (Cytosine-C5)-methyltransferase from HhaI

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKI618

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:15942026%20AND%20SRC:MED&resulttype=core&format=json

OpenCitations bibliographic resource ID

12 January 2020

2224988

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

2 references

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

2224988

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:15942026%20AND%20SRC:MED&resulttype=core&format=json

12 January 2020

PubMed publication ID

15942026

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:15942026%20AND%20SRC:MED&resulttype=core&format=json