Positively charged C-terminal subdomains of EcoRV endonuclease: contributions to DNA binding, bending, and cleavage (Q42392599)

29 October 2017

Positively charged C-terminal subdomains of EcoRV endonuclease: contributions to DNA binding, bending, and cleavage (English)

1 reference

29 October 2017

David A Hiller

1

1 reference

PMCID

2515858

29 October 2017

John J Perona

series ordinal

2

1 reference

PMCID

2515858

29 October 2017

language of work or name

English

0 references

publication date

1 September 2006

1 reference

29 October 2017

1 reference

29 October 2017

45

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29 October 2017

11453-11463

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29 October 2017

38

1 reference

The CCP4 suite: programs for protein crystallography

29 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Bending of adenovirus origin DNA by nuclear factor I as shown by scanning force microscopy is required for optimal DNA replication

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Simultaneous DNA binding and bending by EcoRV endonuclease observed by real-time fluorescence

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

DNA bending and unbending by MutS govern mismatch recognition and specificity

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

DNA recognition by the EcoRV restriction endonuclease probed using base analogues

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Flexible DNA bending in HU-DNA cocrystal structures

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Stopped-flow studies of the kinetics of single-stranded DNA binding and wrapping around the Escherichia coli SSB tetramer

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Charge neutralization and DNA bending by the Escherichia coli catabolite activator protein

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Electrostatics of nanosystems: application to microtubules and the ribosome

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Catalytic efficiency and sequence selectivity of a restriction endonuclease modulated by a distal manganese ion binding site.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Structure of BamHI bound to nonspecific DNA: a model for DNA sliding

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Crystallographic snapshots along a protein-induced DNA-bending pathway

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Divalent metal dependence of site-specific DNA binding by EcoRV endonuclease.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Structural and energetic origins of indirect readout in site-specific DNA cleavage by a restriction endonuclease

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Effects of phosphate neutralization on the shape of the AP-1 transcription factor binding site in duplex DNA.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

DNA binding within the nucleosome core

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Engineering of variants of the restriction endonuclease EcoRV that depend in their cleavage activity on the flexibility of sequences flanking the recognition site

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Role of asymmetric phosphate neutralization in DNA bending by PU.1.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Conformational transitions and structural deformability of EcoRV endonuclease revealed by crystallographic analysis

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Clues and consequences of DNA bending in transcription

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Sequence-specific recognition of cytosine C5 and adenine N6 DNA methyltransferases requires different deformations of DNA.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Probing the indirect readout of the restriction enzyme EcoRV. Mutational analysis of contacts to the DNA backbone

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Structure of the C-terminal end of the nascent peptide influences translation termination

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Solution structure of a cisplatin-induced DNA interstrand cross-link

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Bending of DNA by transcription factors

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

DNA bending by asymmetric phosphate neutralization

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Mg2+ binding to the active site of EcoRV endonuclease: a crystallographic study of complexes with substrate and product DNA at 2 A resolution

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

On the specificity of DNA-protein interactions

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Bending of the bacteriophage lambda attachment site by Escherichia coli integration host factor.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

DNA looping generated by DNA bending protein IHF and the two domains of lambda integrase

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Accuracy of the EcoRI restriction endonuclease: binding and cleavage studies with oligodeoxynucleotide substrates containing degenerate recognition sequences

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

The energetic basis of specificity in the Eco RI endonuclease--DNA interaction.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

The nucleosomal core histone octamer at 3.1 A resolution: a tripartite protein assembly and a left-handed superhelix

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Site-directed mutagenesis studies with EcoRV restriction endonuclease to identify regions involved in recognition and catalysis

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Electron microscopic study of (A)BC excinuclease. DNA is sharply bent in the UvrB-DNA complex

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Asymmetric lateral distribution of unshielded phosphate groups in nucleosomal DNA and its role in DNA bending

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Discrimination between DNA sequences by the EcoRV restriction endonuclease.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Phasing of protein-induced DNA bends in a recombination complex.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Non-cognate enzyme-DNA complex: structural and kinetic analysis of EcoRV endonuclease bound to the EcoRI recognition site GAATTC.

28 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

DNA cleavage by EcoRV endonuclease: two metal ions in three metal ion binding sites.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Electrostatic contributions to site specific DNA cleavage by EcoRV endonuclease.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

The integration host factor of Escherichia coli binds to bent DNA at the origin of replication of the plasmid pSC101.

16 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2515858

Fluorescence resonance energy transfer analysis of the structure of the four-way DNA junction

16 August 2018

1 reference

12 December 2020

A site-directed mutagenesis study to identify amino acid residues involved in the catalytic function of the restriction endonuclease EcoRV

1 reference

12 December 2020

The cleavage site for the restriction endonuclease EcoRV is 5'-GAT/ATC-3'

1 reference

12 December 2020

Rapid, electrostatically assisted association of proteins

1 reference

12 December 2020

Purification and crystallization of the EcoRV restriction endonuclease

1 reference

12 December 2020

Protein-induced bending as a transcriptional switch

1 reference

12 December 2020

Kinetic analysis of a mutational hot spot in the EcoRV restriction endonuclease

1 reference

12 December 2020

Protein-DNA recognition: new perspectives and underlying themes

1 reference

12 December 2020

Static and initiator protein-enhanced bending of DNA at a replication origin

1 reference

12 December 2020

Mechanisms of DNA bending

1 reference

12 December 2020

Thermodynamic origins of specificity in the lac repressor-operator interaction. Adaptability in the recognition of mutant operator sites

1 reference

12 December 2020

Identifiers

DOI

10.1021/BI0606400

1 reference

29 October 2017

1 reference

29 October 2017

1 reference

PMCID

2515858